Sequence-determined dna fragments and corresponding polypeptides encoded thereby

ABSTRACT

The present invention provides DNA molecules that constitute fragments of the genome of a plant, and polypeptides encoded thereby. The DNA molecules are useful for specifying a gene product in cells, either as a promoter or as a protein coding sequence or as an UTR or as a 3′ termination sequence, and are also useful in controlling the behavior of a gene in the chromosome, in controlling the expression of a gene or as tools for genetic mapping, recognizing or isolating identical or related DNA fragments, or identification of a particular individual organism, or for clustering of a group of organisms with a common trait. One of ordinary skill in the art, having this data, can obtain cloned DNA fragments, synthetic DNA fragments or polypeptides constituting desired sequences by recombinant methodology known in the art or described herein.

CROSS REFERENCES TO RELATED APPLICATIONS

This application is a Continuation of co-pending application Ser. No. 11/096,568, filed on Apr. 1, 2005, the entire contents of which are hereby incorporated by reference and for which priority is claimed under 35 U.S.C. §120.

Co-pending application Ser. No. 11/096,568 claims priority under 35 U.S.C. §119(e) on U.S. Provisional Application No. 60/558,095 filed on Apr. 1, 2004, the entire contents of which are also hereby incorporated by reference.

FIELD OF THE INVENTION

The present invention relates to isolated polynucleotides from plants that include a complete coding sequence, or a fragment thereof, that is expressed. In addition, the present invention relates to the polypeptide or protein corresponding to the coding sequence of these polynucleotides. The present invention further relates to the use of these isolated polynucleotides and polypeptides and proteins.

BACKGROUND OF THE INVENTION

There are more than 300,000 species of plants. They show a wide diversity of forms, ranging from delicate liverworts, adapted for life in a damp habitat, to cacti, capable of surviving in the desert. The plant kingdom includes herbaceous plants, such as corn, whose life cycle is measured in months, to the giant redwood tree, which can live for thousands of years. This diversity reflects the adaptations of plants to survive in a wide range of habitats. This is seen most clearly in the flowering plants (phylum Angiospermophyta), which are the most numerous with over 250,000 species. They are also the most widespread, being found from the tropics to the arctic.

The process of plant breeding involving man's intervention in natural breeding and selection is some 20,000 years old. It has produced remarkable advances in adapting existing species to serve new purposes. The world's economics was largely based on the successes of agriculture for most of these 20,000 years.

Plant breeding involves choosing parents, making crosses to allow recombination of genes (alleles) and searching for and selecting improved forms. Success depends on the genes/alleles available, the combinations required and the ability to create and find the correct combinations necessary to give the desired properties to the plant. Molecular genetics technologies are now capable of providing new genes, new alleles and the means of creating and selecting plants with the new, desired characteristics.

When the molecular and genetic basis for different plant characteristics are understood, a wide variety of polynucleotides, both endogenous polynucleotides and created variants, polypeptides, cells, and whole organisms, can be exploited to engineer old and new plant traits in a vast range of organisms including plants. These traits can range from observable morphological characteristics, through adaptation to specific environments to biochemical composition and to molecules that the plants (organisms) exude. Such engineering can involve tailoring existing traits, such as increasing the production of taxol in yew trees, to combining traits from two different plants into a single organism, such as inserting the drought tolerance of a cactus into a corn plant. Molecular and genetic knowledge also allows the creation of new traits. For example, the production of chemicals and pharmaceuticals that are not native to a particular species or the plant kingdom as a whole.

The achievements described in this application were possible because of the results from a cluster of technologies, a genomic engine, depicted below in Schematic 1, that allows information on each gene to be integrated to provide a more comprehensive understanding of gene structure and function and the deployment of genes and gene components to make new products.

I. The Discoveries of the Instant Application

Applicants have isolated and identified genes, gene components and their products and promoters. Specific genes were isolated and/or characterized from Arabidopsis, soybean, maize, wheat and rice. These species were selected because of their economic value and scientific importance and were deliberately chosen to include representatives of the evolutionary divergent dicotyledonous and monocotyledonous groups of the plant kingdom.

The techniques used initially to isolate and characterize most of the genes, namely sequencing of full-length cDNAs, were deliberately chosen to provide information on complete coding sequences and on the complete sequences of their protein products.

Applicants have identified that gene components and products include exons, introns, coding sequences, antisense sequences and terminators. The exons are characterized by the proteins they encode and Arabidopsis.

Further exploitation of molecular genetics technologies enables one to understand the functions and characteristics of each gene and its role in a plant. Three powerful molecular genetics approaches are used to this end:

-   -   (a) Analyses of the phenotypic changes when the particular gene         sequence is activated differentially; (Arabidopsis)     -   (b) Analyses of in what plant organs, to what extent, and in         response to what environmental signals mRNA is synthesized from         the gene; (Arabidopsis and maize) and     -   (c) Analysis of the gene sequence and its relatives. (all         species)

These are conducted using the genomics engine depicted in FIG. 1 that allows information on each gene to be integrated to provide a more comprehensive understanding of gene structure and function and linkage to potential products.

The species Arabidopsis is used extensively in these studies for several reasons: (1) the complete genomic sequence, though poorly annotated in terms of gene recognition, is being produced and published by others and (2) genetic experiments to determine the role of the genes in planta are much quicker to complete.

The phenotypic tables, MA tables, and reference tables and sequence tables indicate the results of these analyses and thus the specific functions and characteristics that are ascribed to the genes and gene components and products.

II. Integration of Discoveries to Provide Scientific Understanding

From the discoveries made, Applicants deduce the biochemical activities, pathways, cellular roles, and developmental and physiological processes that can be modulated using these components. These are discussed and summarized in sections based on the gene function characteristics from the analyses and role in determining phenotypes. These sections illustrate and emphasize that each gene, gene component or product influences biochemical activities, cells or organisms in complex ways, from which there can be many phenotypic consequences.

Furthermore, the development and properties of one part of the plant can be interconnected with other parts. The dependence of shoot and leaf development on root cells is a classic example. Here, shoot growth and development require nutrients supplied from roots, so the protein complement of root cells can affect plant development, including flowers and seed production. Similarly, root development is dependent on the products of photosynthesis from leaves. Therefore, proteins in leaves can influence root developmental physiology and biochemistry.

Thus, the following sections describe both the functions and characteristics of the genes, gene components and products and also the multiplicity of biochemical activities, cellular functions, and the developmental and physiological processes influenced by them.

A. Analyses to Reveal Function and In Vivo Roles of Single Genes in One Plant Species

The genomics engine focuses on individual genes to reveal the multiple functions or characteristics that are associated with each gene, gene components and products of the instant invention in the living plant. For example, the biochemical activity of a protein is deduced based on its similarity to a protein of known function. In this case, the protein may be ascribed with, for example, an oxidase activity. Where and when this same protein is active can be uncovered from differential expression experiments, which show that the mRNA encoding the protein is differentially expressed in response to drought and in seeds but not roots.

Thus, this protein is characterized as a seed protein and drought-responsive oxidase.

B. Analyses to Reveal Function and Roles of Single Genes in Different Species

The genomics engine is used to extrapolate knowledge from one species to many plant species. For example, proteins from different species, capable of performing identical or similar functions, preserve many features of amino acid sequence and structure during evolution. Complete protein sequences are compared and contrasted within and between species to determine the functionally vital domains and signatures characteristic of each of the proteins that is the subject of this application. Thus, functions and characteristics of Arabidopsis proteins are extrapolated to proteins containing similar domains and signatures of corn, soybean, rice and wheat and by implication to all other (plant) species.

C. Analyses Over Multiple Experiments to Reveal Gene Networks and Links Across Species

The genomics engine can identify networks or pathways of genes concerned with the same process and hence linked to the same phenotype(s). Genes specifying functions of the same pathway or developmental environmental responses are frequently co-regulated i.e. they are regulated by mechanisms that result in coincident increases or decreases for all gene members in the group. The Applicants have divided the genes of Arabidopsis and maize into such co-regulated groups on the basis of their expression patterns and the function of each group has been deduced. This process has provided considerable insight into the function and role of thousands of the plant genes in diverse species included in this application.

D. Applications of Applicant's Discoveries

It will be appreciated while reading the sections that the different experimental molecular genetic approaches focused on different aspects of the pathway from gene and gene product through to the properties of tissues, organs and whole organisms growing in specific environments. For each endogenous gene, these pathways are delineated within the existing biology of the species. However, Applicants' inventions allow gene components or products to be mixed and matched to create new genes and placed in other cellular contexts and species, to exhibit new combinations of functions and characteristics not found in nature, or to enhance and modify existing ones. For instance, gene components can be used to achieve expression of a specific protein in a new cell type to introduce new biochemical activities, cellular attributes or developmental and physiological processes. Such cell-specific targeting can be achieved by combining polynucleotides encoding proteins with any one of a large array of promoters to facilitate synthesis of proteins in a selective set of plant cells. This emphasizes that each gene, component and protein can be used to cause multiple and different phenotypic effects depending on the biological context. The utilities are therefore not limited to the existing in vivo roles of the genes, gene components, and gene products.

While the genes, gene components and products disclosed herein can act alone, combinations are useful to modify or modulate different traits. Useful combinations include different polynucleotides and/or gene components or products that have (1) an effect in the same or similar developmental or biochemical pathways; (2) similar biological activities; (3) similar transcription profiles; or (4) similar physiological consequences.

Of particular interest are the transcription factors and key factors in regulatory transduction pathways, which are able to control entire pathways, segments of pathways or large groups of functionally related genes. Therefore, manipulation of such proteins, alone or in combination is especially useful for altering phenotypes or biochemical activities in plants. Because interactions exist between hormone, nutrition, and developmental pathways, combinations of genes and/or gene products from these pathways also are useful to produce more complex changes. In addition to using polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may exhibit different transcription profiles but which participate in common or overlapping pathways. Also, polynucleotides encoding selected enzymes can be combined in novel ways in a plant to create new metabolic pathways and hence new metabolic products.

The utilities of the various genes, gene components and products of the Application are described below in the sections entitled as follows:

III.A. Organ Affecting Genes, Gene Components, Products (Including Differentiation Function)

-   -   III.A.1. Root Genes, Gene Components And Products     -   III.A.2. Root Hair Genes, Gene Components And Products     -   III.A.3. Leaf Genes, Gene Components And Products     -   III.A.4. Trichome Genes And Gene Components     -   III.A.5. Chloroplast Genes And Gene Components     -   III.A.6. Reproduction Genes, Gene Components And Products     -   III.A.7. Ovule Genes, Gene Components And Products     -   III.A.8. Seed And Fruit Development Genes, Gene Components And         Products

III.B. Development Genes, Gene Components And Products

-   -   III.B.1. Imbibition and Germination Responsive Genes, Gene         Components And Products     -   III.B.2. Early Seedling Phase Genes, Gene Components And         Products     -   III.B.3. Size and Stature Genes, Gene Components And Products     -   III.B.4. Shoot-Apical Meristem Genes, Gene Components And         Products     -   III.B.5. Vegetative-Phase Specific Responsive Genes, Gene         Components And Products

III.C. Hormones Responsive Genes, Gene Components And Products

-   -   III.C.1. Abscissic Acid Responsive Genes, Gene Components And         Products     -   III.C.2. Auxin Responsive Genes, Gene Components And Products     -   III.C.3. Brassinosteroid Responsive Genes, Gene Components And         Products     -   III.C.4. Cytokinin Responsive Genes, Gene Components And         Products     -   III.C.5. Gibberellic Acid Responsive Genes, Gene Components And         Products

III.D. Metabolism Affecting Genes, Gene Components And Products

-   -   III.D.1. Nitrogen Responsive Genes, Gene Components And Products     -   III.D.2. Circadian Rhythm Responsive Genes, Gene Components And         Products     -   III.D.3. Blue Light (Phototropism) Responsive Genes, Gene         Components And Products     -   III.D.4. CO₂ Responsive Genes, Gene Components And Products     -   III.D.5. Mitochondria Electron Transport Genes, Gene Components         And Products     -   III.D.6. Protein Degradation Genes, Gene Components And Products     -   III.D.7. Carotenogenesis Responsive Genes, Gene Components And         Products     -   III.D.8. Viability Genes, Gene Components And Products     -   III.D.9. Histone Deacetylase (Axel) Responsive Genes, Gene         Components And Products

III.E. Stress Responsive Genes, Gene Components And Products

-   -   III.E.1. Cold Responsive Genes, Gene Components And Products     -   III.E.2. Heat Responsive Genes, Gene Components And Products     -   III.E.3. Drought Responsive Genes, Gene Components And Products     -   III.E.4. Wounding Responsive Genes, Gene Components And Products     -   III.E.5. Methyl Jasmonate Responsive Genes, Gene Components And         Products     -   III.E.6. Reactive Oxygen Responsive Genes, Gene Components And         H₂O₂ Products     -   III.E.7. Salicylic Acid Responsive Genes, Gene Components And         Products     -   III.E.8. Nitric Oxide Responsive Genes, Gene Components And         Products     -   III.E.9. Osmotic Stress Responsive Genes, Gene Components And         Products     -   III.E.10. Aluminum Responsive Genes, Gene Components And         Products     -   III.E.11. Cadmium Responsive Genes, Gene Components And Products     -   III.E.12. Disease Responsive Genes, Gene Components And Products     -   III.E.13. Defense Responsive Genes, Gene Components And Products     -   III.E.14. Iron Responsive Genes, Gene Components And Products     -   III.E.15. Shade Responsive Genes, Gene Components And Products     -   III.E.16. Sulfur Responsive Genes, Gene Components And Products     -   III.E.17. Zinc Responsive Genes, Gene Components And Products     -   III.E.18. Vigor Responsive Genes, Gene Components And Products     -   III.E.19. Sterol Responsive Genes, Gene Components And Products     -   III.E.20. Branching Responsive Genes, Gene Components And         Products     -   III.E.21 Brittle-Snap Responsive Genes, Gene Components And         Products     -   III.E.22. pH Responsive Genes, Gene Components And Products     -   III.E.23. Guard Cell Responsive Genes, Gene Components And         Products

V. Enhanced Foods SUMMARY OF THE INVENTION

The present invention comprises polynucleotides, such as complete cDNA sequences and/or sequences of genomic DNA encompassing complete genes, fragments of genes, and/or regulatory elements of genes and/or regions with other functions and/or intergenic regions, hereinafter collectively referred to as Sequence-Determined DNA Fragments (SDFs) or sometimes collectively referred to as “genes or gene components”, or sometimes as “genes, gene components or products”, from different plant species, particularly corn, wheat, soybean, rice and Arabidopsis thaliana, and other plants and or mutants, variants, fragments or fusions of said SDFs and polypeptides or proteins derived therefrom. In some instances, the SDFs span the entirety of a protein-coding segment. In some instances, the entirety of an mRNA is represented. Complements of any sequence of the invention are also considered part of the invention.

Other objects of the invention are polynucleotides comprising exon sequences, polynucleotides comprising intron sequences, polynucleotides comprising introns together with exons, intron/exon junction sequences, 5′ untranslated sequences, and 3′ untranslated sequences of the SDFs of the present invention. Polynucleotides representing the joinder of any exons described herein, in any arrangement, for example, to produce a sequence encoding any desirable amino acid sequence are within the scope of the invention.

The present invention also resides in probes useful for isolating and identifying nucleic acids that hybridize to an SDF of the invention. The probes can be of any length, but more typically are 12-2000 nucleotides in length; more typically, 15 to 200 nucleotides long; even more typically, 18 to 100 nucleotides long.

Yet another object of the invention is a method of isolating and/or identifying nucleic acids using the following steps:

(a) contacting a probe of the instant invention with a polynucleotide sample under conditions that permit hybridization and formation of a polynucleotide duplex; and

(b) detecting and/or isolating the duplex of step (a).

The conditions for hybridization can be from low to moderate to high stringency conditions. The sample can include a polynucleotide having a sequence unique in a plant genome. Probes and methods of the invention are useful, for example, without limitation, for mapping of genetic traits and/or for positional cloning of a desired fragment of genomic DNA.

Probes and methods of the invention can also be used for detecting alternatively spliced messages within a species. Probes and methods of the invention can further be used to detect or isolate related genes in other plant species using genomic DNA (gDNA) and/or cDNA libraries. In some instances, especially when longer probes and low to moderate stringency hybridization conditions are used, the probe will hybridize to a plurality of cDNA and/or gDNA sequences of a plant. This approach is useful for isolating representatives of gene families which are identifiable by possession of a common functional domain in the gene product or which have common cis-acting regulatory sequences. This approach is also useful for identifying orthologous genes from other organisms.

The present invention also resides in constructs for modulating the expression of the genes comprised of all or a fragment of an SDF. The constructs comprise all or a fragment of the expressed SDF, or of a complementary sequence. Examples of constructs include ribozymes comprising RNA encoded by an SDF or by a sequence complementary thereto, antisense constructs, constructs comprising coding regions or parts thereof. Such constructs can be constructed using viral, plasmid, bacterial artificial chromosomes (BACs), plasmid artificial chromosomes (PACs), autonomous plant plasmids, plant artificial chromosomes or other types of vectors and exist in the plant as autonomous replicating sequences or as DNA integrated into the genome. When inserted into a host cell the construct is, preferably, functionally integrated with, or operatively linked to, a heterologous polynucleotide. For instance, a coding region from an SDF might be operably linked to a promoter that is functional in a plant.

The present invention also resides in host cells, including bacterial or yeast cells or plant cells, and plants that harbor constructs such as described above. Another aspect of the invention relates to methods for modulating expression of specific genes in plants by expression of the coding sequence of the constructs, by regulation of expression of one or more endogenous genes in a plant or by suppression of expression of the polynucleotides of the invention in a plant. Methods of modulation of gene expression include without limitation (1) inserting into a host cell additional copies of a polynucleotide comprising a coding sequence; (2) inserting antisense or ribozyme constructs into a host cell and (3) inserting into a host cell a polynucleotide comprising a sequence encoding a variant, fragment, or fusion of the native polypeptides of the instant invention.

DETAILED DESCRIPTION OF THE INVENTION I. Description of the Data

As noted above, the Applicants have obtained and analyzed an extensive amount of information on a large number of genes by use of the Ceres Genomic Engine. This information can be categorized into two basic types:

A. Sequence Information for the Inventions

B. Transcriptional Information for the Inventions

I.A. Sequence Information

To harness the potential of the plant genome, Applicants began by elucidating a large number gene sequences, including the sequences of gene components and products, and analyzing the data. The list of sequences and associated data are presented in the Reference and Sequence Tables of the present application (sometimes referred to as the “REF” and “SEQ” Tables). The Reference and Sequence tables include:

-   -   cDNA sequence;     -   coding sequence;     -   5′ & 3′ UTR;     -   transcription start sites;     -   exon and intron boundaries in genomic sequence; and     -   protein sequence.

The Reference and Sequence Tables also include computer-based, comparative analyses between the protein sequences of the invention and sequences with known function. Proteins with similar sequences typically exhibit similar biochemical activities. The Reference table notes:

-   -   sequences of known function that are similar to the Applicants'         proteins; and     -   biochemical activity that is associated with Applicants'         proteins.

Also, by analyzing the protein sequences, Applicants were able to group the protein sequences into groups, wherein all the sequences in the group contain a signature sequence. The groups are presented in the Protein Group Table. The signature sequences are reported in the Protein Group Table. More detailed analyses of the signature sequences are shown in the Protein Group Matrix Table.

To identify gene components and products, Applicants took a cDNA/coding sequence approach. That is, Applicants initiated their studies either by isolating cDNAs and determining their sequences experimentally, or by identifying the coding sequence from genomic sequence with the aid of predictive algorithms. The cDNA sequences and coding sequences also are referred to as “Maximum Length Sequences” in the Reference tables. The cDNA and coding sequences were given this designation to indicate these were the maximum length of coding sequences identified by Applicants.

Due to this cDNA/coding sequence focus of the present application, the Reference and Sequence Tables were organized around cDNA and coding sequences. Each of these Maximum Length Sequences was assigned a unique identifier: Ceres Sequence ID NO, which is reported in the Tables.

All data that relate to these Maximum Length Sequences are grouped together, including 5′ & 3′ UTRs; transcription start sites; exon and intron boundaries in genomic sequence; protein sequence, etc.

Below, a more detailed explanation of the organization of the Reference and Sequence Tables and how the data in the tables were generated is provided.

a. cDNA

Applicants have ascertained the sequences of mRNAs from different organisms by reverse transcription of mRNA to DNA, which was cloned and then sequenced. These complementary DNA or cDNA sequences also are referred to as Maximum Length Sequences in the Reference Tables, which contain details on each of the sequences in the Sequence Tables.

Each sequence was assigned a Pat. Appln. Sequence ID NO: and an internal Ceres Sequence ID NO: as reported in the Reference Table, the section labeled “(Ac) cDNA Sequence.” An example is shown below:

-   -   Max Len. Seq.:     -   (Ac) cDNA Sequence         -   Pat. Appln. Sequence ID NO: 174538         -   Ceres Sequence ID NO: 5673127

Both numbers are included in the Sequence Table to aid in tracking of information, as shown below:

<210> 174538 (Pat. Appln. Sequence ID NO:) <211> 1846 <212> DNA (genomic) <213> Arabidopsisthaliana <220> <221> misc_feature <222> (1) . . . (1846) <223> Ceres Seq. ID no. 5673127 <220> <221> misc_feature <222> ( ) . . . ( ) <223> n is a, c, t, g, unknown, or other <400> 174538 acaagaacaa caaaacagag gaagaagaag aagaagatga agcttctggc tctgtttcca 60 tttctagcga tcgtgatcca actcagctgt . . . etc.

The Sequence and Reference Tables are divided into sections by organism: Arabidopsis thaliana, Brassica napus, Glycine max, Zea mays, Triticum aestivum; and Oryza sativa.

b. Coding Sequence

The coding sequence portion of the cDNA was identified by using computer-based algorithms and comparative biology. The sequence of each coding sequence of the cDNA is reported in the “PolyP Sequence” section of the Reference Tables, which are also divided into sections by organism. An example shown below for the peptides that relate to the cDNA sequence above

PolyP Sequence

Pat. Appln. Sequence ID NO 174539

Ceres Sequence ID NO 5673128

Loc. Sequence ID NO 174538: @ 1 nt.

Loc. Sig. P. Sequence ID NO 174539: @ 37 aa.

The polypeptide sequence can be found in the Sequence Tables by either the Pat. Appln. Sequence ID NO or by the Ceres Sequence ID NO: as shown below:

<210> 174539 (Pat. Appln. Sequence ID NO) <211> 443 <212> PRT <213> Arabidopsis thaliana <220> <221> peptide <222> (1) . . . (443) <223> Ceres Seq. ID no. 5673128 <220> <221> misc_feature <222> ( ) . . . ( ) <223> xaa is any aa, unknown or other <400> 174539 Thr Arg Thr Thr Lys Gln Arg Lys Lys Lys Lys Lys Met Lys Leu Leu 1        5            10          15 Ala Leu Phe Pro Phe Leu Ala Ile . . . etc.                 25

The PolyP section also indicates where the coding region begins in the Maximum Length Sequence. More than one coding region may be indicated for a single polypeptide due to multiple potential translation start codons. Coding sequences were identified also by analyzing genomic sequence by predictive algorithms, without the actual cloning of a cDNA molecule from an mRNA. By default, the cDNA sequence was considered the same as the coding sequence, when Maximum Length Sequence was spliced together from a genomic annotation.

C. 5′ and 3′ UTR

The 5′ UTR can be identified as any sequence 5′ of the initiating codon of the coding sequence in the cDNA sequence. Similarly, the 3′ UTR is any sequence 3′ of the terminating codon of the coding sequence.

d. Transcription Start Sites

Applicants cloned a number of cDNAs that encompassed the same coding sequence but comprised 5′ UTRs of different lengths. These different lengths revealed the multiple transcription start sites of the gene that corresponded to the cDNA. These multiple transcription start sites are reported in the “Sequence # w. TSS” section” of the Reference Tables.

e. Exons & Introns

Alignment of the cDNA sequences and coding portions to genomic sequence permitted Applicants to pinpoint the exon/intron boundaries. These boundaries are identified in the Reference Table under the “Pub gDNA” section. That section reports the gi number of the public BAC sequence that contains the introns and exons of interest. An example is shown below:

Max Len. Seq.:

Pub gDNA:

-   -   gi No: 1000000005     -   Gen. seq. in cDNA:         -   115777 . . . 115448 by Method #1         -   115105 . . . 114911 by Method #1         -   114822 . . . 114700 by Method #1         -   114588 . . . 114386 by Method #1         -   114295 . . . 113851 by Method #1         -   115777 . . . 115448 by Method #2         -   115105 . . . 114911 by Method #2         -   114822 . . . 114700 by Method #2         -   114588 . . . 114386 by Method #2         -   114295 . . . 113851 by Method #2         -   115813 . . . 115448 by Method #3         -   115105 . . . 114911 by Method #3         -   114822 . . . 114700 by Method #3         -   114588 . . . 114386 by Method #3         -   114295 . . . 113337 by Method #3

(Ac) cDNA Sequence

All the gi numbers were assigned by Genbank to track the public genomic sequences except:

gi 1000000001

gi 1000000002

gi 1000000003

gi 1000000004; and

gi 1000000005.

These gi numbers were assigned by Applicants to the five Arabidopsis chromosome sequences that were published by the Institute of Genome Research (TIGR). Gi 1000000001 corresponds to chromosome 1, Gi 1000000002 to chromosome 2, etc.

The method of annotation is indicated as well as any similar public annotations.

f. Promoters & Terminators

Promoter sequences are 5′ of the translational start site in a gene; more typically, 5′ of the transcriptional start site or sites. Terminator sequences are 3′ of the translational terminator codon; more typically, 3′ of the end of the 3′ UTR.

For even more specifics of the Reference and Sequence Tables, see the section below titled “Brief Description of the Tables.”

I.B. Transcriptional (Differential Expression) Information—Introduction to Differential Expression Data & Analyses

A major way that a cell controls its response to internal or external stimuli is by regulating the rate of transcription of specific genes. For example, the differentiation of cells during organogenensis into forms characteristic of the organ is associated with the selective activation and repression of large numbers of genes. Thus, specific organs, tissues and cells are functionally distinct due to the different populations of mRNAs and protein products they possess. Internal signals program the selective activation and repression programs. For example, internally synthesized hormones produce such signals. The level of hormone can be raised by increasing the level of transcription of genes encoding proteins concerned with hormone synthesis.

To measure how a cell reacts to internal and/or external stimuli, individual mRNA levels can be measured and used as an indicator for the extent of transcription of the gene. Cells can be exposed to a stimulus, and mRNA can be isolated and assayed at different time points after stimulation. The mRNA from the stimulated cells can be compared to control cells that were not stimulated. The mRNA levels of particular Maxiumum Length Sequences that are higher in the stimulated cell versus the control indicate a stimulus-specific response of the cell. The same is true of mRNA levels that are lower in stimulated cells versus the control condition.

Similar studies can be performed with cells taken from an organism with a defined mutation in their genome as compared with cells without the mutation. Altered mRNA levels in the mutated cells indicate how the mutation causes transcriptional changes. These transcriptional changes are associated with the phenotype that the mutated cells exhibit that is different from the phenotype exhibited by the control cells.

Applicants use microarray techniques to measure the levels of mRNAs in cells from mutant plants, stimulated plants, and/or selected from specific organs. The differential expression of various genes in the samples versus controls are listed in the MA Tables.

a. Experimental Detail

A microarray is a small solid support, usually the size of a microscope slide, onto which a number of polynucleotides have been spotted onto or synthesized in distinct positions on the slide (also referred to as a chip). Typically, the polynucleotides are spotted in a grid formation. The polynucleotides can either be Maximum Length Sequences or shorter synthetic oligonucleotides, whose sequence is complementary to specific Maximum Length Sequence entities. A typical chip format is as follows:

Oligo #1 Oligo #2 Oligo #3 Oligo #4 Oligo #5 Oligo #6 Oligo #7 Oligo #8 Oligo #9

For Applicants' experiments, samples are hybridized to the chips using the “two-color” microarray procedure. A fluorescent dye is used to label cDNA reverse-transcribed from mRNA isolated from cells that had been stimulated, mutated, or collected from a specific organ or developmental stage. A second fluorescent dye of another color is used to label cDNA prepared from control cells.

The two differentially-labeled cDNAs are mixed together. Microarray chips are incubated with this mixture. For Applicants' experiments, the two dyes that are used are Cy3, which fluoresces in the red color range, and Cy5, which fluoresces in the green/blue color range. Thus, if:

cDNA#1 binds to Oligo #1;

cDNA#1 from the sample is labeled red;

cDNA#1 from the control is labeled green, and

cDNA#1 is in both the sample and control,

then cDNA#1 from both the sample and control will bind to Oligo#1 on the chip. If the sample has 10 times more cDNA#1 than the control, then 10 times more of the cDNA#1 would be hybridized to Oligo#1. Thus, the spot on the chip with Oligo#1 spot would look red.

Oligo #1 Oligo #2 Oligo #3 Oligo #4 Oligo #5 Oligo #6 Oligo #7 Oligo #8 Oligo #9 If the situation were reversed, the spot would appear green. If the sample has approximately the same amount of cDNA#1 as the control, then the Oligo#1 spot on the chip would look yellow. These color differentials are measured quantitatively and used to deduce the relative concentration of mRNAs from individual genes in particular samples.

b. MA Table

To generate data, Applicants label and hybridize the sample and control mRNA in duplicate experiments. One chip is exposed to a mixture of cDNAs from both a sample and control, where the sample cDNA is labeled with Cy3, and the control is labeled with Cy5 dye. For the second labeling and chip hybridization experiments, the fluorescent labels are reversed; that is, the Cy5 dye is used for the sample, and the Cy3 dye is used for the control.

Whether Cy5 or Cy3 is used to label the sample, the fluorescence produced by the sample is divided by the fluorescence of the control. A cDNA is determined to be differentially expressed in response to the stimulus in question if a statistically-significantly ratio difference in the sample versus the control is measured by both chip hybridization experiments.

The MA tables show which cDNA is significantly up-regulated as designated by a “+” and which is significantly down-regulated as designated by a “−” for each pair of chips using the same sample and control.

I.D. Brief Description of the Data Contained in the Sequence Listing-Miscellaneous Feature Field

1. Reference and Sequence Data

The sequences of exemplary SDFs and polypeptides corresponding to the coding sequences of the instant invention are described in the Sequence Listing. The Miscellaneous Feature field of the Sequence Listing contains data associated with the particular sequence. For example, it may refer to a number of “Maximum Length Sequences” or “MLS.” Each MLS corresponds to the longest cDNA obtained, either by cloning or by the prediction from genomic sequence. The sequence of the MLS is the cDNA sequence as described in the Av subsection of the miscellaneous feature field.

The Miscellaneous Feature field also includes the following information relating to each MLS:

I. cDNA Sequence

-   -   A. 5′UTR     -   B. Coding Sequence     -   C. 3′UTR

II. Genomic Sequence

-   -   A. Exons     -   B. Introns     -   C. Promoters

III. Link of cDNA Sequences to Clone IDs

IV. Multiple Transcription Start Sites

V. Polypeptide Sequences

-   -   A. Signal Peptide     -   B. Domains     -   C. Related Polypeptides

VI. Related Polynucleotide Sequences

I. cDNA Sequence

Indicates which sequence in the Sequence Listing represents the sequence of each MLS. The MLS sequence can comprise 5′ and 3′ UTR as well as coding sequences. In addition, specific cDNA clone numbers also are included when the MLS sequence relates to a specific cDNA clone.

A. 5′UTR

The location of the 5′ UTR can be determined by comparing the most 5′ MLS sequence with the corresponding genomic sequence as indicated in the miscellaneous feature field. The sequence that matches, beginning at any of the transcriptional start sites and ending at the last nucleotide before any of the translational start sites corresponds to the 5′ UTR.

B. Coding Region

The coding region is the sequence in any open reading frame found in the MLS. Coding regions of interest are indicated in the PolyP SEQ subsection.

C. 3′UTR

The location of the 3′ UTR can be determined by comparing the most 3′ MLS sequence with the corresponding genomic sequence. The sequence that matches, beginning at the translational stop site and ending at the last nucleotide of the MLS corresponds to the 3′ UTR.

II. Genomic Sequence

Further, the miscellaneous feature field indicates the specific “gi” number of the genomic sequence if the sequence resides in a public databank. For each genomic sequence, the miscellaneous feature field indicates which regions are included in the MLS. These regions can include the 5′ and 3′ UTRs as well as the coding sequence of the MLS. See, for example, the scheme below:

The first and last base of each region that is included in an MLS sequence is reported. An example is shown below:

gi No. 47000:

37102 . . . 37497

37593 . . . 37925

The numbers indicate that the MLS contains the following sequences from two regions of gi No. 47000; a first region including bases 37102-37497, and a second region including bases 37593-37925.

A. Exon Sequences

The location of the exons can be determined by comparing the sequence of the regions from the genomic sequences with the corresponding MLS sequence.

i. Initial Exon

To determine the location of the initial exon, information from the

(1) polypeptide sequence section;

(2) cDNA polynucleotide section; and

(3) the genomic sequence section

is used. First, the polypeptide section indicates where the translational start site is located in the MLS sequence. The MLS sequence can be matched to the genomic sequence that corresponds to the MLS. Based on the match between the MLS and corresponding genomic sequences, the location of the translational start site can be determined in one of the regions of the genomic sequence. The location of this translational start site is the start of the first exon.

Generally, the last base of the exon of the corresponding genomic region, in which the translational start site is located, will represent the end of the initial exon. In some cases, the initial exon ends with a stop codon, when the initial exon is the only exon.

In the case when sequences representing the MLS are in the positive strand of the corresponding genomic sequence, the last base will be a larger number than the first base. When the sequences representing the MLS are in the negative strand of the corresponding genomic sequence, then the last base will be a smaller number than the first base.

ii. Internal Exons

Except for the regions that comprise the 5′ and 3′ UTRs, initial exon, and terminal exon, the remaining genomic regions that match the MLS sequence are the internal exons. Specifically, the bases defining the boundaries of the remaining regions also define the intron/exon junctions of the internal exons.

iii. Terminal Exon

As with the initial exon, the location of the terminal exon is determined with information from the

(1) polypeptide sequence section;

(2) cDNA polynucleotide section; and

(3) the genomic sequence section.

The polypeptide section will indicate where the stop codon is located in the MLS sequence. The MLS sequence can be matched to the corresponding genomic sequence. Based on the match between MLS and corresponding genomic sequences, the location of the stop codon can be determined in one of the regions of the genomic sequence. The location of this stop codon is the end of the terminal exon. Generally, the first base of the exon of the corresponding genomic region that matches the cDNA sequence, in which the stop codon is located, will represent the beginning of the terminal exon. In some cases, the translational start site represents the start of the terminal exon, which is the only exon.

In the case when the MLS sequences are in the positive strand of the corresponding genomic sequence, the last base will be a larger number than the first base. When the MLS sequences are in the negative strand of the corresponding genomic sequence, then the last base will be a smaller number than the first base.

B. Intron Sequences

In addition, the introns corresponding to the MLS are defined by identifying the genomic sequence located between the regions where the genomic sequence comprises exons. Thus, introns are defined as starting one base downstream of a genomic region comprising an exon, and end one base upstream from a genomic region comprising an exon.

C. Promoter Sequences

As indicated below, promoter sequences corresponding to the MLS are defined as sequences upstream of the first exon; more usually, as sequences upstream of the first of multiple transcription start sites; even more usually as sequences about 2,000 nucleotides upstream of the first of multiple transcription start sites.

III. Link of cDNA Sequences to Clone IDs

As noted above, the cDNA clone(s) that relate to each MLS are identified. The MLS sequence can be longer than the sequences included in the cDNA clones. In such a case the region of the MLS that is included in the clone is indicated. If either the 5′ or 3′ termini of the cDNA clone sequence is the same as the MLS sequence, no mention will be made.

IV. Multiple Transcription Start Sites

Initiation of transcription can occur at a number of sites of the gene. The possible multiple transcription sites for each gene is indicated and the location of the transcription start sites can be either a positive or negative number.

The positions indicated by positive numbers refer to the transcription start sites as located in the MLS sequence. The negative numbers indicate the transcription start site within the genomic sequence that corresponds to the MLS.

To determine the location of the transcription start sites with the negative numbers, the MLS sequence is aligned with the corresponding genomic sequence. In the instances when a public genomic sequence is referenced, the relevant corresponding genomic sequence can be found by direct reference to the nucleotide sequence indicated by the “gi” number shown in the public genomic DNA section. When the position is a negative number, the transcription start site is located in the corresponding genomic sequence upstream of the base that matches the beginning of the MLS sequence in the alignment. The negative number is relative to the first base of the MLS sequence that matches the genomic sequence corresponding to the relevant “gi” number.

In the instances when no public genomic DNA is referenced, the relevant nucleotide sequence for alignment is the nucleotide sequence associated with the amino acid sequence designated by “gi” number of the later PolyP SEQ subsection.

V. Polypeptide Sequences

The PolyP SEQ subsection lists SEQ ID NOs and Ceres SEQ ID NO for polypeptide sequences corresponding to the coding sequence of the MLS sequence and the location of the translational start site with the coding sequence of the MLS sequence.

The MLS sequence can have multiple translational start sites and can be capable of producing more than one polypeptide sequence.

A. Signal Peptide

The miscellaneous feature field also indicates in subsection (B) the cleavage site of the putative signal peptide of the polypeptide corresponding to the coding sequence of the MLS sequence. Typically, signal peptide coding sequences comprise a sequence encoding the first residue of the polypeptide to the cleavage site residue.

B. Domains

Subsection (C) provides information regarding identified domains (where present) within the polypeptide and (where present) a name for the polypeptide domain.

C. Related Polypeptides

Subsection (Dp) provides (where present) information concerning amino acid sequences that are found to be related and have some percentage of sequence identity to the polypeptide sequences. Each of these related sequences is identified by a “gi” number.

VI. Related Polynucleotide Sequences

Subsection (Dn) provides polynucleotide sequences (where present) that are related to and have some percentage of sequence identity to the MLS or corresponding genomic sequence.

Abbreviation Description Max Len. Seq. Maximum Length Sequence rel to Related to Clone Ids Clone ID numbers Pub gDNA Public Genomic DNA gi No. gi number Gen. Seq. in Cdna Genomic Sequence in cDNA (Each region for a single gene prediction is listed on a separate line. In the case of multiple gene predictions, the group of regions relating to a single prediction are separated by a blank line) (Ac) cDNA SEQ cDNA sequence Pat. Appln. SEQ ID NO Patent Application SEQ ID NO: Ceres SEQ ID NO: Ceres SEQ ID NO: 1673877 SEQ # w. TSS Location within the cDNA sequence, SEQ ID NO:, of Transcription Start Sites which are listed below Clone ID #: # -> # Clone ID comprises bases # to # of the cDNA Sequence PolyP SEQ Polypeptide Sequence Pat. Appln. SEQ ID NO: Patent Application SEQ ID NO: Ceres SEQ ID NO Ceres SEQ ID NO: Loc. SEQ ID NO: @ nt. Location of translational start site in cDNA of SEQ ID NO: at nucleotide number (C) Pred. PP Nom. & Nomination and Annotation of Domains within Annot. Predicted Polypeptide(s) (Title) Name of Domain Loc. SEQ ID NO #: # -> Location of the domain within the polypeptide # aa. of SEQ ID NO: from # to # amino acid residues. (Dp) Rel. AA SEQ Related Amino Acid Sequences Align. NO Alignment number gi No Gi number Desp. Description % Idnt. Percent identity Align. Len. Alignment Length Loc. SEQ ID NO: # -> Location within SEQ ID NO: from # to # # aa amino acid residue.

2. MA_DIFF DATA

The MA_diff data present in the Miscellaneous features field presents the results of the differential expression experiments for the mRNAs, as reported by their corresponding cDNA ID number, that were differentially transcribed under a particular set of conditions as compared to a control sample.

The Table is organized according to each set of experimental conditions, which are denoted by the term “Expt ID:” followed by a particular number. The table below links each Expt ID with a short description of the experiment and the parameters.

The first column contains the cDNA ID number, which corresponds to those utilized in the Sequence Listing and Miscellaneous Features fields. This identification number is followed by the “Expt ID” identifier. Next, the differential expression under those particular conditions is shown. Here, increases in mRNA abundance levels in experimental plants versus the controls are denoted with the number one (1). Likewise, reductions in mRNA abundance levels in the experimental plants are denoted with the number minus one (−1). Lastly, the utility of the sequence is noted.

MA_diff (Experiment) Table

The following Table summarizes the experimental procedures utilized for the differential expression experiments, each experiment being identified by a unique “Expt ID” number.

Experiment short name genome EXPT_ID Value PARAMETER UNITS 3642-1 Arabidopsis 108512 3746-1 Plant Line Hours Arab_0.001%_MeJA_1 Arabidopsis 108568 Aerial Tissue Tissue 0.001%_MeJA Treatment Compound 1 Timepoint Hours Arab_0.001%_MeJA_1 Arabidopsis 108569 Aerial Tissue Tissue 6 Timepoint Hours 0.001%_MeJA Treatment Compound Arab_0.1uM_Epi- Arabidopsis 108580 Aerial Tissue Tissue Brass_1 1 Timepoint Hours 0.1uM_Brassino_Steroid Treatment Compound Arab_0.1uM_Epi- Arabidopsis 108581 Aerial Tissue Tissue Brass_1 6 Timepoint Hours 0.1uM_Brassino_Steroid Treatment Compound Arab_100uM_ABA_1 Arabidopsis 108560 Aerial Tissue Tissue 1 Timepoint Hours 100uM_ABA Treatment Compound Arab_100uM_ABA_1 Arabidopsis 108561 Aerial Tissue Tissue 100uM_ABA Treatment Compound 6 Timepoint Hours Arab_100uM_BA_1 Arabidopsis 108566 Aerial Tissue Tissue 1 Timepoint Hours 100uM_BA Treatment Compound Arab_100uM_BA_1 Arabidopsis 108567 Aerial Tissue Tissue 100uM_BA Treatment Compound 6 Timepoint Hours Arab_100uM_GA3_1 Arabidopsis 108562 Aerial Tissue Tissue 1 Timepoint Hours 100uM GA3 Treatment Compound Arab_100uM_GA3_1 Arabidopsis 108563 Aerial Tissue Tissue 100uM GA3 Treatment Compound 6 Timepoint Hours Arab_100uM_NAA_1 Arabidopsis 108564 Aerial Tissue Tissue 1 Timepoint Hours 100uM_NAA Treatment Compound Arab_100uM_NAA_1 Arabidopsis 108565 Aerial Tissue Tissue 100uM_NAA Treatment Compound 6 Timepoint Hours Arab_20%_PEG_1 Arabidopsis 108570 Aerial Tissue Tissue 1 Timepoint Hours 20% PEG Treatment Compound Arab_20%_PEG_1 Arabidopsis 108571 Aerial Tissue Tissue 20% PEG Treatment Compound 6 Timepoint Hours Arab_2mM_SA_1 Arabidopsis 108586 Aerial Tissue Tissue 2mM_SA Treatment Compound 1 Timepoint Hours Arab_2mM_SA_1 Arabidopsis 108587 Aerial Tissue Tissue 6 Timepoint Hours 2mM_SA Treatment Compound Arab_5mM_H2O2_1 Arabidopsis 108582 Aerial Tissue Tissue 1 Timepoint Hours 5mM_H2O2 Treatment Compound Arab_5mM_H2O2_1 Arabidopsis 108583 Aerial Tissue Tissue 5mM_H2O2 Treatment Compound 6 Timepoint Hours Arab_5mM_NaNP_1 Arabidopsis 108584 Aerial Tissue Tissue 1 Timepoint Hours 5mM_NaNP Treatment Compound Arab_5mM_NaNP_1 Arabidopsis 108585 Aerial Tissue Tissue 5mM_NaNP Treatment Compound 6 Timepoint Hours Arab_Cold_1 Arabidopsis 108578 Aerial Tissue Tissue Cold Treatment Compound 1 Timepoint Hours Arab_Cold_1 Arabidopsis 108579 Aerial Tissue Tissue 6 Timepoint Hours Cold Treatment Compound Arab_Drought_1 Arabidopsis 108572 Aerial Tissue Tissue 1 Timepoint Hours Drought Treatment Compound Arab_Drought_1 Arabidopsis 108573 Aerial Tissue Tissue Drought Treatment Compound 6 Timepoint Hours Arab_Heat_1 Arabidopsis 108576 Aerial Tissue Tissue 1 Timepoint Hours Heat (42 deg Treatment Compound C) Arab_Heat_1 Arabidopsis 108577 Aerial Tissue Tissue Heat (42 deg Treatment Compound C) 6 Timepoint Hours Arab_Ler- Arabidopsis 108595 Ler_pi Plant Line Hours pi_ovule_1 Ovule Tissue Tissue Arab_Ler- Arabidopsis 108594 Ler_rhl Plant Line Hours rhl_root_1 Root Tissue Tissue Arab_NO3_H- Arabidopsis 108592 Aerial Tissue Tissue to-L_1 Low Nitrogen Treatment Compound 12 Timepoint Hours Arab_NO3_H- Arabidopsis 108593 Aerial Tissue Tissue to-L_1 24 Timepoint Hours Low Nitrogen Treatment Compound Arab_NO3_L- Arabidopsis 108588 Aerial Tissue Tissue to-H_1 2 Timepoint Hours Nitrogen Treatment Compound Arab_NO3_L- Arabidopsis 108589 Aerial Tissue Tissue to-H_1 Nitrogen Treatment Compound 6 Timepoint Hours Arab_NO3_L- Arabidopsis 108590 Aerial Tissue Tissue to-H_1 9 Timepoint Hours Nitrogen Treatment Compound Arab_NO3_L- Arabidopsis 108591 Aerial Tissue Tissue to-H_1 Nitrogen Treatment Compound 12 Timepoint Hours Arab_Wounding_1 Arabidopsis 108574 Aerial Tissue Tissue 1 Timepoint Hours Wounding Treatment Compound Arab_Wounding_1 Arabidopsis 108575 Aerial Tissue Tissue Wounding Treatment Compound 6 Timepoint Hours Columbia/CS3726 Arabidopsis 108475 Columbia species Hours flower SA SA Treatment Compound 5 weeks Timepoint Hours Columbia/CS3726 Arabidopsis 108476 CS3726 species Hours flower SA 5 weeks Timepoint Hours SA Treatment Compound Corn_0.001Percent_MeJA Zea Mays 108555 Aerial Tissue Tissue 24 Timepoint Hours 0.001%_MeJA Treatment Compound Corn_0.1uM_Brassino_Steroid Zea Mays 108557 24 Timepoint Hours Aerial Tissue Tissue 0.1uM_Brassino_Steroid Treatment Compound Corn_100uM_ABA Zea Mays 108513 Aerial Tissue Tissue ABA Treatment Compound 6 Timepoint Hours Corn_100uM_ABA Zea Mays 108597 Aerial Tissue Tissue 24 Timepoint Hours 100uM_ABA Treatment Compound Corn_100uM_BA Zea Mays 108517 Aerial Tissue Tissue 6 Timepoint Hours BA Treatment Compound Corn_100uM_GA3 Zea Mays 108519 Aerial Tissue Tissue 100uM Treatment Compound Giberillic Acid 1 Timepoint Hours Corn_100uM_GA3 Zea Mays 108520 Aerial Tissue Tissue 6 Timepoint Hours 100uM Treatment Compound Giberillic Acid Corn_100uM_GA3 Zea Mays 108521 Aerial Tissue Tissue 100uM Treatment Compound Giberillic Acid 12 Timepoint Hours Corn_100uM_NAA Zea Mays 108516 Aerial Tissue Tissue NAA Treatment Compound 6 Timepoint Hours Corn_100uM_NAA Zea Mays 108554 Aerial Tissue Tissue 24 Timepoint Hours NAA Treatment Compound Corn_1400- Zea Mays 108598 Shoot apices Tissue Tissue 6/S-17 Corn_150mM_NaCl Zea Mays 108541 Aerial Tissue Tissue 1 Timepoint Hours 150mM_NaCl Treatment Compound Corn_150mM_NaCl Zea Mays 108542 Aerial Tissue Tissue 150mM_NaCl Treatment Compound 6 Timepoint Hours Corn_150mM_NaCl Zea Mays 108553 Aerial Tissue Tissue 24 Timepoint Hours 150mM_NaCl Treatment Compound Corn_20%_PEG Zea Mays 108539 Aerial Tissue Tissue 1 Timepoint Hours 20% PEG Treatment Compound Corn_20%_PEG Zea Mays 108540 Aerial Tissue Tissue 20% PEG Treatment Compound 6 Timepoint Hours Corn_2mM_SA Zea Mays 108515 Aerial Tissue Tissue SA Treatment Compound 12 Timepoint Hours Corn_2mM_SA Zea Mays 108552 Aerial Tissue Tissue SA Treatment Compound 24 Timepoint Hours Corn_5mM_H2O2 Zea Mays 108537 Aerial Tissue Tissue H2O2 Treatment Compound 1 Timepoint Hours Corn_5mM_H2O2 Zea Mays 108538 Aerial Tissue Tissue 6 Timepoint Hours H2O2 Treatment Compound Corn_5mM_H2O2 Zea Mays 108558 Aerial Tissue Tissue 24 Timepoint Hours H2O2 Treatment Compound Corn_5mM_NO Zea Mays 108526 Aerial Tissue Tissue NO Treatment Compound 1 Timepoint Hours Corn_5mM_NO Zea Mays 108527 Aerial Tissue Tissue 6 Timepoint Hours NO Treatment Compound Corn_5mM_NO Zea Mays 108559 Aerial Tissue Tissue 12 Timepoint Hours NO Treatment Compound Corn_Cold Zea Mays 108533 Aerial Tissue Tissue 1 Timepoint Hours Cold Treatment Compound Corn_Cold Zea Mays 108534 Aerial Tissue Tissue Cold Treatment Compound 6 Timepoint Hours Corn_Drought Zea Mays 108502 Drought Treatment Compound 1 Timepoint Hours Corn_Drought Zea Mays 108503 Drought Treatment Compound 6 Timepoint Hours Corn_Drought Zea Mays 108504 Drought Treatment Compound 12 Timepoint Hours Corn_Drought Zea Mays 108556 Drought Treatment Compound 24 Timepoint Hours Corn_Heat Zea Mays 108522 Aerial Tissue Tissue 1 Timepoint Hours Heat (42 deg Treatment Compound C.) Corn_Heat Zea Mays 108523 Aerial Tissue Tissue 6 Timepoint Hours Heat (42 deg Treatment Compound C.) Corn_Imbibed Zea Mays 108518 Imbibed Treatment Compound Seeds 4 Age days old Roots Tissue Tissue Corn_Imbibed Zea Mays 108528 Imbibed Treatment Compound Seeds Aerial Tissue Tissue 5 Age days old Corn_Imbibed Zea Mays 108529 Imbibed Treatment Compound Seeds 5 Age days old Root Tissue Tissue Corn_Imbibed Zea Mays 108530 Imbibed Treatment Compound Seeds Aerial Tissue Tissue 6 Age days old Corn_Imbibed Zea Mays 108531 Imbibed Treatment Compound Seeds 6 Age days old root Tissue Tissue Corn_Imbibed Zea Mays 108545 Imbibed Treatment Compound Seeds Aerial Tissue Tissue 3 Age days old Corn_Imbibed Zea Mays 108546 Imbibed Treatment Compound Seeds 3 Age days old Root Tissue Tissue Corn_Imbibed Zea Mays 108547 Imbibed Treatment Compound Seeds Aerial Tissue Tissue 4 Age days old Corn_Imbibed_Embryo_Endosperm Zea Mays 108543 2 Age days old Imbibed Treatment Compound Embryo Tissue Tissue Corn_Imbibed_Embryo_Endosperm Zea Mays 108544 2 Age days old Endosperm Tissue Tissue Imbibed Treatment Compound Corn_Meristem Zea Mays 108535 Root Tissue Tissue Meristem 192 Timepoint Hours Corn_Meristem Zea Mays 108536 Shoot Tissue Tissue Meristem 192 Timepoint Hours Corn_Nitrogen_H_to_L Zea Mays 108532 Roots Tissue Tissue Low Nitrogen Treatment Compound 16 Timepoint Hours Corn_Nitrogen_H_to_L Zea Mays 108548 Root Tissue Tissue Low Nitrogen Treatment Compound 4 Timepoint Hours Corn_Nitrogen_L_to_H Zea Mays 108549 Aerial Tissue Tissue 0.166 Timepoint Hours Nitrogen Treatment Compound Corn_Nitrogen_L_to_H Zea Mays 108550 Aerial Tissue Tissue Nitrogen Treatment Compound 1.5 Timepoint Hours Corn_Nitrogen_L_to_H Zea Mays 108551 Aerial Tissue Tissue 3 Timepoint Hours Nitrogen Treatment Compound Corn_RT1 Zea Mays 108599 Unknown Plant Line Hours Root Tissue Tissue Corn_Wounding Zea Mays 108524 Aerial Tissue Tissue Wounding Treatment Compound 1 Timepoint Hours Corn_Wounding Zea Mays 108525 Aerial Tissue Tissue 6 Timepoint Hours Wounding Treatment Compound Drought_Flowers Arabidopsis 108473 Flowers Tissue Tissue 7 d Timepoint Hours Drought Treatment Compound Drought_Flowers Arabidopsis 108474 Flowers Tissue Tissue Drought Treatment Compound 8 d (1d- Timepoint Hours post_re- watering) GA Treated Arabidopsis 108484 1 Timepoint Hours 1 Timepoint Hours GA Treated Arabidopsis 108485 6 Timepoint Hours 6 Timepoint Hours GA Treated Arabidopsis 108486 12 Timepoint Hours 12 Timepoint Hours Germinating Arabidopsis 108461 Day 1 Timepoint Hours Seeds Germinating Arabidopsis 108462 Day 2 Timepoint Hours Seeds Germinating Arabidopsis 108463 Day 3 Timepoint Hours Seeds Germinating Arabidopsis 108464 Day 4 Timepoint Hours Seeds Herbicide V3.1 Arabidopsis 108465 Round up Treatment Compound 12 Timepoint Hours Herbicide V3.1 Arabidopsis 108466 Trimec Treatment Compound 12 Timepoint Hours Herbicide V3.1 Arabidopsis 108467 Finale Treatment Compound 12 Timepoint Hours Herbicide V3.1 Arabidopsis 108468 Glean Treatment Compound 12 Timepoint Hours Herbicide_v2 Arabidopsis 107871 Finale Treatment Compound 4 Timepoint Hours Herbicide_v2 Arabidopsis 107876 Finale Treatment Compound 12 Timepoint Hours Herbicide_v2 Arabidopsis 107881 Glean Treatment Compound 4 Timepoint Hours Herbicide_v2 Arabidopsis 107886 Trimec Treatment Compound 4 Timepoint Hours Herbicide_v2 Arabidopsis 107891 Trimec Treatment Compound 12 Timepoint Hours Herbicide_v2 Arabidopsis 107896 Round-up Treatment Compound 4 Timepoint Hours Trichome Arabidopsis 108452 Hairy Tissue Tissue Inflorescences Influorescence expt #1 SA treatment_1 Arabidopsis 108471 Columbia Species Hours hour 1 Timepoint Hours SA Treatment Compound SA treatment_1 Arabidopsis 108472 CS3726 Species Hours hour 1 Timepoint Hours SA Treatment Compound SA treatment_4 Arabidopsis 108469 columbia Species Hours hour 4 Timepoint Hours SA Treatment Compound SA treatment_4 Arabidopsis 108470 CS3726 Species Hours hour SA Treatment Compound 4 Timepoint Hours SA Arabidopsis 107953 50 Probe % of treatment_AJ Amount Standard Amount SA Treatment Compound 24 Timepoint Hours Clontech Probe Type Probe method SA Arabidopsis 107960 50 Probe % of treatment_AJ Amount Standard Amount SA Treatment Compound 24 Timepoint Hours Operon Probe Type Probe method SA_treatment Arabidopsis 108443 SA Treatment Compound 24 hour 24 Timepoint Hours SA_treatment 6 Arabidopsis 108440 SA treatment Treatment Compound hour 6 hour CS3726 species Hours SA_treatment 6 Arabidopsis 108441 SA treatment Treatment Compound hour 6 hour Columbia species Hours Nitrogen High Arabidopsis 108454 10 min Timepoint Hours transition to Low Nitrogen High Arabidopsis 108455 1 hr Timepoint Hours transition to Low BR_Shoot Arabidopsis 108478 dwf4-1 Plant Line Hours Apices Expt BR_Shoot Arabidopsis 108479 AOD4-4 Plant Line Hours Apices Expt BR_Shoot Arabidopsis 108480 Ws-2 Plant Line Hours Apices Expt BL Treatment Compound BR_Shoot Arabidopsis 108481 Ws-2 Plant Line Hours Apices Expt BRZ Treatment Compound Tissue Specific Arabidopsis 108429 green flower Tissue Tissue Expression operon Probe Type Probe method 50 Probe % of Amount Standard Amount Tissue Specific Arabidopsis 108430 white flower Tissue Tissue Expression 50 Probe % of Amount Standard Amount operon Probe Type Probe method Tissue Specific Arabidopsis 108431 flowers (bud) Tissue Tissue Expression operon Probe Type Probe method 50 Probe % of Amount Standard Amount Tissue Specific Arabidopsis 108436 5-10 mm Tissue Tissue Expression siliques 33 Probe % of Amount Standard Amount operon Probe Type Probe method Tissue Specific Arabidopsis 108437 <5 mm Tissue Tissue Expression siliques operon Probe Type Probe method 33 Probe % of Amount Standard Amount Tissue Specific Arabidopsis 108438 5 wk siliques Tissue Tissue Expression 33 Probe % of Amount Standard Amount operon Probe Type Probe method Tissue Specific Arabidopsis 108439 Roots (2 wk) Tissue Tissue Expression operon Probe Type Probe method 33 Probe % of Amount Standard Amount Tissue Specific Arabidopsis 108497 3 week Tissue Tissue Expression Rossette leaves 100 Probe % of Amount Standard Amount operon Probe Type Probe method Tissue Specific Arabidopsis 108498 3-week stems Tissue Tissue Expression operon Probe Type Probe method 100 Probe % of Amount Standard Amount U.A.E. Arabidopsis 108451 13B12 Plant Line Hours Knockout Ws Arabidopsis Arabidopsis 108477 stems and Tissue Tissue Drought 2 days leaves 2 days Timepoint Hours Ws Arabidopsis Arabidopsis 108482 4 days Timepoint Hours Drought 4 days Ws Arabidopsis Arabidopsis 108483 6 days Timepoint Hours Drought 6 days ap2-floral buds Arabidopsis 108501 ap2 (Ler.) Plant Line Hours floral buds Tissue Tissue nitrogen-seed Arabidopsis 108487 0.5 Timepoint Hours set nitrogen-seed Arabidopsis 108488 2 Timepoint Hours set nitrogen-seed Arabidopsis 108489 4 Timepoint Hours set rh1 mutant2 Arabidopsis 108433 mutant Tissue Tissue root tips Arabidopsis 108434 root tips Tissue Tissue stm mutants Arabidopsis 108435 stem Tissue Tissue Aluminum SMD 7304, SMD 7305 Axel SMD 6654, SMD 6655 Cadium SMD 7427, SMD 7428 Cauliflower SMD 5329, SMD 5330 Chloroplast SMD 8093, SMD 8094 Circadian SMD 2344, SMD 2359, SMD 2361, SMD 2362, SMD 2363, SMD 2364, SMD 2365, SMD 2366, SMD 2367, SMD 2368, SMD 3242 CO2 SMD7561, SMD 7562, SMD 7261, SMD 7263, SMD 3710, SMD 4649, SMD 4650 Disease SMD 7342, SMD 7343 reactive oxygen SMD 7523 Iron SMD 7114, SMD 7115, SMD 7125 defense SMD 8031, SMD 8032 Mitchondria- SMD Electron 8061, Transport SMD 8063 NAA SMD 3743, SMD 3749, SMD 6338, SMD 6339 Nitrogen SMD 3787, SMD 3789 Phototropism SMD 4188, SMD 6617, SMD 6619 Shade SMD 8130, SMD 7230 Sqn SMD 7133, SMD 7137 Sulfur SMD 8034, SMD 8035 Wounding SMD 3714, SMD 3715 Zinc SMD 7310, SMD 7311

3. Protein Domain Data

The Protein Domain data, located in the Miscellaneous Feature field of the Sequence Listing, provides details concerning the protein domains. The majority of the protein domain descriptions given are obtained from Prosite and Pfam, which are available on the internet. Each description begins with the pfam and Prosite identifying numbers, the full name of the domain, and a detailed description, including biological and in vivo implications/functions for the domain, references which further describe such implications/functions, and references that describe tests/assays to measure the implications/functions.

4. Ortholog List Data

This data, also located in the miscellaneous feature field of the Sequence Listing, lists pairs of orthologs that were identified using the T Blast X program. Each column contains a cDNA_id number corresponding to a sequence from Arabidopsis, wheat, corn, soybean or canola. The sequence corresponding to all cDNA_id numbers can be found in either the Sequence Listing or the Miscellaneous Feature field.

II. How the Inventions Reveal how Genes, Gene Components and Products Function

The different experimental molecular genetic approaches focused on different aspects of genes, gene components, and gene products of the inventions. The variety of the data demonstrates the multiple functions and characteristics of single genes, gene components, and products. The data also explain the pathways and networks in which individual genes and products participate and interact. As a result, the circumstances or conditions are now known when these genes and networks are active. These new understandings of biology are relevant for many plant species. The following section describes the process by which Applicants analyze the experimental results relavent to the present invention.

II.A. Experimental Results Reveal Many Facets of a Single Gene

The experimental results are used to dissect the function of individual components and products of the genes. For example, the biochemical activity of the encoded protein is surmised from sequence analyses, and promoter specificity is identified through transcriptional analyses. Generally, the data presented herein is used to functionally annotate either the protein sequence and/or the regulatory sequence that controls transcription and translation.

II.A.1. Functions of Coding Sequences Revealed by the Ceres Genomic Engine

II.A.1.a. Sequence Similarity to Proteins of Known Function can be Used to Associate Biochemical Activities and Molecular Interaction to the Proteins of the Invention

The protein sequences of the invention are analyzed to determine if they shared any sequence characteristics with proteins of known activity. Proteins are grouped together based on sequence similarity, either localized or throughout the length of the proteins. Typically, such groups of proteins exhibit common biochemical activities or interact with similar molecules.

II.A.1.a.1. Presence of Amino Acid Motifs Indicates Biological Function

Localized protein sequence similarity, also referred to as amino acid motifs, have been attributed to enzyme or protein functions. A library of motifs, important for function, have been documented in PROSITE, a public database available on the internet. This library includes descriptions of the motifs and their functions. The zinc finger motif is one such entry in PROSITE, which reports that the zinc finger domain of DNA-binding proteins is typically defined by a 25-30 amino acid motif containing specific cysteine or histidine residues that are involved in the tetrahedral coordination of a zinc ion. Any protein comprising a sequence similar to the zinc finger amino acid motif will have similar functional activity (specific binding of DNA).

Protein sequences of the invention have been compared to a library of amino acid motifs in the pFAM database, which is linked to the PROSITE database. If any of Applicants' protein sequences exhibit similarity to these amino acid motifs or domains, the Reference Table notes the name and location of the motif in the “Pred. PP Nom. & Annot” section of the Reference tables For example, polypeptide, CERES Sequence ID NO: 1545823 is associated with zinc finger motif as follows in the Reference Table:

(C) Pred. PP Nom. & Annot.

-   -   Zinc finger, C3HC4 type (RING finger)     -   Loc. Sequence ID NO 133059: 58->106 aa.

II.A.1.a.2. Related Amino Acid Sequences Share Similar Biological Functions

When studying protein sequence families, it is apparent that some regions have been better conserved than others during evolution. These regions are generally important for the function of a protein and/or for the maintenance of its three-dimensional structure.

The Reference Table reports in section “(Dp) Rel. AA Sequence” when a protein shares amino acid similarity with a protein of known activity. The section reports the gi number of the protein of known activity, a brief description of the activity, and the location where it shares sequence similarity to Applicants' polypeptide sequence.

Using this analysis, biochemical activity of the known protein is associated with Applicants' proteins. An example for the polypeptide described above is as follows:

(Dp) Rel. AA Sequence

-   -   Align. NO 524716     -   gi No 2502079     -   Desp.: (AF022391) immediate early protein; ICP0 [Feline         herpesvirus 1]     -   % Idnt.: 33.7     -   Align. Len.: 87     -   Loc. Sequence ID NO 133059: 52->137 aa.

II.A.1.b. Differential Expression Results Explain in which Cellular Responses the Proteins of the Invention are Involved

Differential expression results show when the coding sequence is transcribed, and therefore when the activity of the protein is deployed by the cell. Similar coding sequences can have very different physiological consequences because the sequences are expressed at different times or places, rather than because of any differences in protein activity. Therefore, modified levels (increased or decreased) of expression as compared to a control provide an indication of the function of a corresponding gene, gene components, and gene products.

These experiments can determine which are genes “over-expressed” under a given stimulus. Such over-expressed genes give rise to higher transcript levels in a plant or cell that is stimulated as compared to the transcript levels of the same genes in a control organism or cell. Similarly, differential expression experiments can reveal “under-expressed” genes.

To increase the cellular response to a stimulus, additional copies of the coding sequences of a gene that is over-expressed are inserted into a cell. Increasing transcript levels of an over-expressed gene can heighten or prolong the particular cellular response. A similar enhancement can occur when transcription of an under-expressed gene is inhibited. In contrast, the cellular response will be shortened or less severe when the over-expressed genes are inhibited or when expression of the under-expressed genes are increased.

In addition to analyzing the levels of transcription, the data are also analyzed to gain insight into the changes in transcription over time. That is, while the plants in the experiments were reacting to either an external or internal stimulus, a differential experiment takes a snapshot of the transcription levels in the cells at one specific time. However, a number of snap-shots can be taken at different time points during an external stimulus regime, or at different stages of development during an internal stimulus. These results show how the plant changes transcription levels over time, and therefore protein levels, in response to specific stimuli to produce phenotypic changes. These results show that a protein is implicated in a single, but more likely, in a number of cellular responses.

II.A.1.b.1. The Transcript Levels of a Protein Over Time in Response to a Stimuli are Revealed by Transcriptional Analyses Over Many Experiments

Applicants produce data from plants at different times after a specific stimulus. These results show whether the expression level of a gene spikes at a key moment during the cellular response, or whether the transcript level remains constant. Thus, coding sequences are not only determined to be over- or under-expressed, but are also classified by the initial timing and duration of differential expression. This understanding of timing is used to increase or decrease any desired cellular response.

Generally, Applicants assay plants at 2 to 4 different time points after exposing the plants to the desired stimuli. From these experiments, “early” and “late” responders are identified. These labels are applied to either the regulatory sequences driving transcription of the gene as well as to the protein encoded by the gene.

The following example illustrates how the genes, gene components and products are classified as either early or late responders following a specific treatment. The mRNAs from plants exposed to drought conditions are isolated 1 hour and 6 hours after exposure to drought conditions. These mRNAs are tested utilizing microarray techniques. The graph below illuminates possible transcription profiles over the time course, plotting all the (+) data points as +1 and all the (−) data points as −1:

-   -   (The value for each time point is determined using a pair of         microarray chips as described above.)

Data acquired from this type of time course experiment are useful to understand how to increase or decrease the speed of the cellular response. Inserting extra copies of the coding sequence of early responders into a cell in order to over-express the specific gene triggers a faster cellular response. Alternatively, coding sequences of late responders that are over-expressed are placed under the control of promoters of early responders as another means to increase the cellular response.

Inserting anti-sense or sense mRNA suppression constructs of the early responders that are over-expressed retards action of the late responders, thereby delaying the desired cellular response. In another embodiment, extra copies of the promoters of both early and late responders are added to inhibit expression of both types of over-expressed genes.

-   -   The experiments described herein are grouped together to         determine the time course of the transcript levels of different         coding sequences in response to different stimuli.

II.A.1.b.2. The Transcript Levels of a Protein Over Different Developmental Stages can be Identified by Transcriptional Analyses Over Many Experiments

Differential expression data are produced for different development stages of various organs and tissues. Measurement of transcript levels divulges whether specific genes give rise to spikes of transcription at specific times during development, or whether transcription levels remain constant. This understanding is used to increase speed of development, or to arrest development at a specific stage.

Like the time-course experiments, the developmental stage data classifies genes as being transcribed at early or late stages of development. Generally, Applicants assay different organs or tissues at 2-4 different stages.

Inhibiting under-expressed genes at either early or late stages triggers faster development times. The overall development time is also increased by this means to allow organs and tissue to grow to a larger size or to allow more organs or tissues to be produced. Alternatively, coding sequences of late stage genes that are under-expressed are placed under the control of promoters of early stage genes to increase development.

Inserting extra copies of the coding sequence of early stage genes that are under-expressed retards action of the late-stage genes and delays the desired development.

Fruit development of Arabidopsis is one example. Siliques of varying sizes, which are representative of different stages, are assayed by microarray techniques. Specifically, mRNA is isolated from siliques between 0-5 mm, between 5-10 mm and >10 mm in length.

This graph shows the expression pattern of a cell wall synthesis gene, cDNAID 1595707, during fruit development.

The developmental course shows that the gene encoding a cell wall synthesis protein is up-regulated when the fruit is 0-5 mm, but returns to normal levels at 5-10 mm and >10 mm. Increase of cell wall synthesis leads to larger cells and/or greater number of cells. This type of increase boosts fruit yield. The coding sequence of the cell wall synthesis protein under the control of a strong early stage promoter increases fruit size or number.

A pectinesterase gene, cDNA ID 1396123, is also differentially expressed during fruit development. Pectinesterase catalyzes the hydrolysis of pectin into pectate and methanol. This biochemical activity plays an important role in cell wall metabolism during fruit ripening. To shorten the time for fruit ripening, extra copies of this gene with its endogenous promoter are inserted into a desired plant. With its native promoter, the extra copies of the gene are expressed at the normal time, to promote extra pectinesterase at the optimal stage of fruit development and thereby shorten ripening time.

II.A.1.b.3. Proteins that are Common in a Number of Similar Responses can be Identified by Transcriptional Analyses Over a Number of Experiments

The differential expression experiments also reveal the genes, and therefore the coding sequence, that are common to a number of cellular responses. By identifying the genes that are differentially expressed in a number of similar responses, the genes at the nexus of a range of responses are discovered. For example, genes that are differentially expressed in all the stress responses are at the hub of many of the stress response pathways.

These types of nexus genes, proteins, and pathways are differentially expressed in many or a majority of the responses or developmental conditions of interest. Typically, a nexus gene, protein or pathway is differentially expressed in generally the same direction in many or majority of all the desired experiments. By doing so, the nexus gene is responsible for triggering the same or similar set of pathways or networks for various cellular responses. This type of gene is useful in modulating pleiotropic effects or triggering or inhibiting a general class of responses.

When nexus genes are differentially expressed in a set of responses, but in different directions, these data indicate that a nexus gene is responsible for creating the specificity in a response by triggering the same pathway, but to a different degree. Placing such nexus genes under a constitutive promoter to express the proteins at a more constant level removes the fluctuations. For example, a plant that is better drought adapted, but not cold adapted is modified to be tolerant to both conditions by placing a nexus gene that is up-regulated in drought but down regulated in cold under the control of a constitutive promoter.

II.A.1.b.4. Proteins that are Common to Disparate Responses can be Identified by Transcriptional Analyses Over a Number of Experiments

Phenotypes and traits result from complex interactions between cellular pathways and networks. The pathways that are linked by expression of common genes to specify particular traits is discerned by identifying the genes that show differential expression of seemingly disparate responses or developmental stages. For example, hormone fluxes in a plant direct cell patterning and organ development. Genes that are differentially expressed both in the hormone experiments and organ development experiments are of particular interest to control plant development.

II.A.1.c. Observations of Phenotypic Changes Show What Physiological Consequences Applicants' Proteins can Produce

Another direct means of determining the physiological consequences of a protein is to make aberrant decreases or increases of its expression level in a cell. To this end, Applicants produce plants that include an extra expressed copy of the gene. The plants are then planted under various conditions to determine if any visible physiological changes are caused. These changes then are attributed to the changes in protein levels.

II.B. Experimental Results Also Reveal the Functions of Genes

II.B.1. Linking Signature Sequences to Conservation of Biochemical Activities and Molecular Interactions

Proteins that possess the same defined domains or motifs are likely to carry out the same biochemical activity or interact with a similar class of target molecule, e.g., DNA, RNA, proteins, etc. Thus, the pFAM domains listed in the Reference Tables are routinely used as predictors of these properties. Substrates and products for the specific reactions vary from protein to protein. Where the substrates, ligands, or other molecules bound are identical, the affinities may differ between the proteins. Typically, the affinities exhibited by different functional equivalents varies no more than 50%; more typically, no more than 25%; even more typically, no more than 10%; or even less.

Proteins with very similar biochemical activities or molecular interactions share similar structural properties, such as substrate grooves, as well as sequence similarity in more than one motif. Usually, the proteins share at least two motifs of the signature sequence; more usually, three motifs; even more usually four motifs or greater. Typically, the proteins exhibit 70% sequence identity in the shared motifs; more typically, 80% sequence identity; even more typically, 90%, 95%, 96%, 97%, 98% or 99% sequence identity or greater. These proteins also often share sequence similarity in the variable regions between the constant motif regions. Further, the shared motifs are in the same order from amino- to carboxyl-termini. The length of the variable regions between the motifs in these proteins, generally, is similar. Specifically, the number of residues between the shared motifs in these proteins varies by less than 25%; more usually, varies by less than 20%; even more usually, less than 15%; even more usually less than 10% or even less.

II.B.2. Linking Signature Sequences to Conservation of Cellular Responses or Activities

Proteins that exhibit similar cellular responses or activities will possess the structural and conserved domain/motifs as described in the Biochemical Activities and Molecular Interactions above.

Proteins play a larger role in cellular response than just their biochemical activities or molecular interactions suggest. For example, a protein can initiate gene transcription that is specific to the drought response of a cell. Other cellular responses and activities include: stress responses, hormonal responses, growth and differential of a cell, cell to cell interactions, etc.

The cellular role or activities of a protein are deduced by transcriptional analyses or phenotypic analyses as well as by determining the biochemical activities and molecular interactions of the protein. For example, transcriptional analyses indicate that transcription of gene A is greatly increased during flower development. Such data implicates protein A, encoded by gene A, in the process of flower development. Proteins that share sequence similarity in more than one motif also act as functional equivalents for protein A during flower development.

III. Description of the Genes, Gene Components and Products, Together with their Use and Application

As described herein, Applicants provide an understanding of the function and phenotypic implications of the genes, gene components and products of the present invention. Bioinformatic analysis provides such information. The sections of the present application containing the bioinformatic analysis, together with the Sequence and Reference Tables, teach those skilled in the art how to use the genes, gene components and products of the present invention to provide plants with novel characteristics. Similarly, differential expression analysis provides additional such information and the sections of the present application on that analysis describe the functions of the genes, gene components and products of the present invention which are understood from the results of the differential expression experiments. The same is true with respect to the phenotype data, where the results of the Knock-in experiments and the sections of the present application on those experiments provide the skilled artisan with further description of the functions of the genes, gene components and products of the present invention.

As a result, one reading each of these sections of the present application as an independent report will understand the function of the genes, gene components and products of the present invention. But those sections and descriptions can also be read in combination, in an integrated manner, to gain further insight into the functions and uses for the genes, gene components and products of the present invention. Such an integrated analysis does not require extending beyond the teachings of the present application, but rather combining and integrating the teachings depending upon the particular purpose of the reader.

Some sections of the present application describe the function of genes, gene components and products of the present invention with reference to the type of plant tissue (e.g. root genes, leaf genes, etc.), while other sections describe the function of the genes, gene components and products with respect to responses under certain conditions (e.g. Auxin-responsive genes, heat-responsive genes, etc.). Thus, if one desires to utilize a gene understood from the application to be a particular tissue-type of gene, then the condition-specific responsiveness of that gene is understood from the differential expression tables, and very specific characteristics of actions of that gene in a transformed plant is understood by recognizing the overlap or intersection of the gene functions as understood from the two different types of information. Thus, for example, if one desires to transform a plant with a root gene for enhancing root growth and performance, one knows the useful root genes from the results reported in the knock-in table. A review of the differential expression data also shows that a specific root gene is over-expressed in response to heat and osmotic stress as well. The function of that gene is then described in (1) the section of the present application that discusses root genes, (2) the section of the present application that discusses heat-responsive genes, and (3) the section of the application that discusses osmotic stress-responsive genes. The function(s) that are commonly described in those three sections are then particularly characteristic of a plant transformed with that gene. This type of integrated analysis of data is viewed from the following schematic that summarizes, for one particular gene, the function of that gene as understood from the phenotype and differential expression experiments.

Gene function known Gene function known Gene function known from phenotype from first differential from second differential experiments expression experiment expression experiment Function A Function A Function A Function B Function C Function C Function D Function E Function F Function F Function F Function G Function G Function H Function I Function I Function J

In the above example, one skilled in the art will understand that a plant transformed with this particular gene particularly exhibits functions A and F because those are the functions which are understood in common from the three different experiments.

Similar analyses can be conducted on various genes of the present invention, by which one skilled in the art effectively modulates plant functions depending upon the particular use or conditions envisioned for the plant.

III.A. Organ-Affecting Genes, Gene Components, Products (Including Differentiation and Function)

III.A.1. Root Genes, Gene Components and Products

The economic values of roots arise not only from harvested adventitious roots or tubers, but also from the ability of roots to funnel nutrients to support growth of all plants and increase their vegetative material, seeds, fruits, etc. Roots have four main functions. First, they anchor the plant in the soil. Second, they facilitate and regulate the molecular signals and molecular traffic between the plant, soil, and soil fauna. Third, the root provides a plant with nutrients gained from the soil or growth medium. Fourth, they condition local soil chemical and physical properties.

Root genes are active or potentially active to a greater extent in roots than in most other organs of the plant. These genes and gene products regulate many plant traits from yield to stress tolerance. Root genes are used to modulate root growth and development.

III.A.2. Root Hair Genes, Gene Components and Products

Root hairs are specialized outgrowths of single epidermal cells termed trichoblasts. In many and perhaps all species of plants, the trichoblasts are regularly arranged around the perimeter of the root. In Arabidopsis, for example, trichoblasts tend to alternate with non-hair cells or atrichoblasts. This spatial patterning of the root epidermis is under genetic control, and a variety of mutants have been isolated in which this spacing is altered or in which root hairs are completely absent, such as the rhl mutant. Some surface cells of roots develop into single epidermal cells termed trichoblasts or root hairs. Some of the root hairs persist for the life of the plant; others gradually die back and some cease to function due to external influences.

Root hairs are also sites of intense chemical and biological activity and as a result strongly modify the soil they contact. Some roots hairs are coated with surfactants and/or mucilage to facilitate these activities. Specifically, roots hairs are responsible for nutrient uptake by mobilizing and assimilating water, reluctant ions, organic and inorganic compounds and chemicals. In addition, they attract and interact with beneficial microfauna and flora. Root hairs also help to mitigate the effects of toxic ions, pathogens and stress. Examples of root hair properties and activities that root hairs modulate include root hair surfactant and mucilage, nutrient uptake, microbe and nematode associations, oxygen transpiration; detoxification effects of iron, aluminum, cadium, mercury, salt, and other soil constituents, pathogens, glucosinolates, changes in soil and rhizosheath.

The root and root hairs uptake of the nutrients contributes to a source-sink effect in a plant. The greater the source of nutrients, the more sinks, such as stems, leaves, flowers, seeds, fruits, etc. can draw sustenance to grow. Thus, root hair genes modulate the vigor and yield of the plant overall, as well as of distinct cells, organs, or tissues of a plant.

III.A.3. Leaf Genes, Gene Components and Products

Leaves are responsible for producing most of the fixed carbon in a plant and are critical to plant productivity and survival. Great variability in leaf shapes and sizes is observed in nature. Leaves also exhibit varying degrees of complexity, ranging from simple to multi-compound. Leaf genes, as defined here, not only modulate leaf morphology, but also influence the shoot apical meristem, thereby affecting leaf arrangement on the shoot, internodes, nodes, axillary buds, photosynthetic capacity, carbon fixation, photorespiration and starch synthesis. Leaf genes elucidated here are used to modify a number of traits of economic interest including leaf shape, plant yield, stress tolerance, and to modify both the efficiency of synthesis and accumulation of specific metabolites and macromolecules (including carbohydrates, proteins, oils, waxes, etc).

III.A.4. Reproduction Genes, Gene Components and Products

Reproduction genes are defined as genes or components of genes capable of modulating any aspect of sexual reproduction from flowering time and inflorescence development to fertilization and finally seed and fruit development. These genes are of great economic interest as well as biological importance. The fruit and vegetable industry grosses over $1 billion USD a year. The seed market, valued at approximately $15 billion USD annually, is even more lucrative.

Inflorescence and Floral Development Genes, Gene Components and Products

During reproductive growth the plant enters a program of floral development that culminates in fertilization, followed by the production of seeds. Senescence may or may not follow. Flower formation is a precondition for the sexual propagation of plants and is therefore essential for propagation of plants that cannot be propagated vegetatively, as well as for the formation of seeds and fruits. The point of time at which the vegetative growth of plants changes into flower formation is of vital importance in agriculture, horticulture and plant breeding. Also, the number of flowers is often of economic importance, for example in the case of various useful plants (tomato, cucumber, zucchini, cotton etc.) where an increased number of flowers leads to an increased yield, or in the case of ornamental plants and cut flowers.

Flowering plants exhibit one of two types of inflorescence architecture: (1) indeterminate, in which the inflorescence grows indefinitely, or (2) determinate, in which a terminal flower is produced. Adult organs of flowering plants develop from groups of stem cells called meristems. The identity of a meristem is inferred from structures it produces: vegetative meristems give rise to roots and leaves, inflorescence meristems give rise to flower meristems, and flower meristems give rise to floral organs such as sepals and petals. Not only are meristems capable of generating new meristems of a different identity, but their own identity can change during development. For example, a vegetative shoot meristem can be transformed into an inflorescence meristem upon floral induction, and in some species, the inflorescence meristem itself will eventually become a flower meristem. Despite the importance of meristem transitions in plant development, little is known about the underlying mechanisms.

Following germination, the shoot meristem produces a series of leaf meristems on its flanks. However, once floral induction has occurred, the shoot meristem switches to the production of flower meristems. Flower meristems produce floral organ primordia, which individually develop into sepals, petals, stamens or carpels. Thus, flower formation can be thought of as a series of distinct developmental steps, i.e. floral induction, the formation of flower primordia and the production of flower organs. Mutations disrupting each of the steps have been isolated in a variety of species, suggesting that a genetic hierarchy directs the flowering process (see for review, Weigel and Meyerowitz, In Molecular Basis of Morphogenesis (ed. M. Bernfield). 51st Annual Symposium of the Society for Developmental Biology, pp. 93-107, New York, 1993).

Expression of many reproduction genes and gene products is orchestrated by internal programs or the surrounding environment of a plant. These genes used to modulate traits such as fruit and seed yield

Seed and Fruit Development Genes, Gene Components and Products

The ovule is the primary female sexual reproductive organ of flowering plants. At maturity it contains the egg cell and one large central cell containing two polar nuclei encased by two integuments that, after fertilization, develop into the embryo, endosperm and seed coat of the mature seed, respectively. As the ovule develops into the seed, the ovary matures into the fruit or silique. As such, seed and fruit development requires the orchestrated transcription of numerous polynucleotides, some of which are ubiquitous, others that are embryo-specific and still others that are expressed only in the endosperm, seed coat or fruit. Such genes are termed fruit development responsive genes and are used to modulate seed and fruit growth and development such as seed size, seed yield, seed composition and seed dormancy.

III.A.5. Ovule Genes, Gene Components and Products

The ovule is the primary female sexual reproductive organ of flowering plants. It contains the egg cell and, after fertilization occurs, contains the developing seed. Consequently, the ovule is at times comprised of haploid, diploid and triploid tissue. As such, ovule development requires the orchestrated transcription of numerous polynucleotides, some of which are ubiquitous, others that are ovule-specific and still others that are expressed only in the haploid, diploid or triploid cells of the ovule.

Although the morphology of the ovule is well known, little is known of these polynucleotides and polynucleotide products. Mutants allow identification of genes that participate in ovule development. As an example, the pistillata (PI) mutant replaces stamens with carpels, thereby increasing the number of ovules present in the flower. Accordingly, comparison of transcription levels between the wild-type and PI mutants allows identification of ovule-specific developmental polynucleotides.

Ovule genes are useful to modulate egg cell development, ovule maturation, metabolism, polar nuclei, fusion, central cell, maturation, metabolism, synergids, maturation, programmed cell death, nucellus, maturation, integuments, maturation, funiculus, extension, cuticle, maturation, tensile properties, ovule, modulation of ovule senescence and shaping.

III.A.6. Seed and Fruit Development Genes, Gene Components and Products

The ovule is the primary female sexual reproductive organ of flowering plants. At maturity it contains the egg cell and one large central cell containing two polar nuclei encased by two integuments that, after fertilization, develop into the embryo, endosperm and seed coat of the mature seed, respectively. As the ovule develops into the seed, the ovary matures into the fruit or silique. As such, seed and fruit development requires the orchestrated transcription of numerous polynucleotides, some of which are ubiquitous, others that are embryo-specific and still others that are expressed only in the endosperm, seed coat or fruit. Such genes are termed fruit development responsive genes and are used to modulate seed and fruit growth and development such as seed size, seed yield, seed composition and seed dormancy.

III.B. Development Genes, Gene Components and Products

III.B.1. Imbibition and Germination Responsive Genes, Gene Components and Products Imbibition and Germination Responsive Genes, Gene Components and Products

Seeds are a vital component of the world's diet. Cereal grains alone, which comprise ˜90% of all cultivated seeds, contribute up to half of the global per capita energy intake. The primary organ system for seed production in flowering plants is the ovule. At maturity, the ovule consists of a haploid female gametophyte or embryo sac surrounded by several layers of maternal tissue including the nucellous and the integuments. The embryo sac typically contains seven cells including the egg cell, two synergids, a large central cell containing two polar nuclei, and three antipodal cells. Pollination results in the fertilization of both egg and central cell. The fertilized egg develops into the embryo. The fertilized central cell develops into the endosperm. And the integuments mature into the seed coat. As the ovule develops into the seed, the ovary matures into the fruit or silique. Late in development, the developing seed ends a period of extensive biosynthetic and cellular activity and begins to desiccate to complete its development and enter a dormant, metabolically quiescent state. Seed dormancy is generally an undesirable characteristic in agricultural crops, where rapid germination and growth are required. Some degree of dormancy is advantageous, however, at least during seed development. This is particularly true for cereal crops because it prevents germination of grains while still on the ear of the parent plant (preharvest sprouting), a phenomenon that results in major losses to the agricultural industry. Extensive domestication and breeding of crop species have ostensibly reduced the level of dormancy mechanisms present in the seeds of their wild ancestors, although under some adverse environmental conditions, dormancy may reappear. By contrast, weed seeds frequently mature with inherent dormancy mechanisms that allow some seeds to persist in the soil for many years before completing germination.

Germination commences with imbibition, the uptake of water by the dry seed, and the activation of the quiescent embryo and endosperm. The result is a burst of intense metabolic activity. At the cellular level, the genome is transformed from an inactive state to one of intense transcriptional activity. Stored lipids, carbohydrates and proteins are catabolized fueling seedling growth and development. DNA and organelles are repaired, replicated and begin functioning. Cell expansion and cell division are triggered. The shoot and root apical meristems are activated and begin growth and organogenesis. Germination is complete when a part of the embryo, the radicle, extends to penetrate the structures that surround it. In Arabidopsis, seed germination takes place within twenty-four (24) hours after imbibition. As such, germination requires the rapid and orchestrated transcription of numerous polynucleotides. Germination is followed by expansion of the hypocotyl and opening of the cotyledons. Meristem development continues to promote root growth and shoot growth, which is followed by early leaf formation.

Imbibition and Germination Genes

Imbibition and germination includes those events that commence with the uptake of water by the quiescent dry seed and terminate with the expansion and elongation of the shoots and roots. The germination period exists from imbibition to when part of the embryo, usually the radicle, extends to penetrate the seed coat that surrounds it. Imbibition and germination genes are defined as genes, gene components and products that modulate one or more processes of imbibition and germination described above. They are useful to modulate many plant traits from early vigor to yield to stress tolerance.

III.B.2. Early Seedling-Phase Specific Responsive Genes, Gene Components and Products

A few days after germination is complete, which is also referred to as the early seedling phase, is one of the more active stages of the plant life cycle. During this period the plant begins development and growth of the first leaves, roots, and other organs not found in the embryo. Generally this stage begins when germination ends. The first sign that germination has been completed is usually an increase in length and fresh weight of the radicle. Such genes and gene products can regulate a number of plant traits to modulate yield. For example, these genes are active or potentially active to a greater extent in developing and rapidly growing cells, tissues and organs, as exemplified by development and growth of a seedling 3 or 4 days after planting a seed.

Rapid, efficient establishment of a seedling is very important in commercial agriculture and horticulture. It is also vital that resources are approximately partitioned between shoot and root to facilitate adaptive growth. Phototropism and geotropism need to be established. All these require post-germination process to be sustained to ensure that vigorous seedlings are produced. Early seedling phase genes, gene components and products are useful to manipulate these and other processes.

III.B.3. Shoot-Apical Meristem Genes, Gene Components and Products

New organs, stems, leaves, branches and inflorescences develop from the stem apical meristem (SAM). The growth structure and architecture of the plant therefore depends on the behavior of SAMs. SAMs are comprised of a number of morphologically undifferentiated, dividing cells located at the tips of shoots. SAM genes elucidated here modify the activity of SAMs and thereby many traits of economic interest from ornamental leaf shape to organ number to responses to plant density.

In addition, a key attribute of the SAM is its capacity for self-renewal. Thus, SAM genes of the instant invention are useful for modulating one or more processes of SAM structure and/or function including (I) cell size and division; (II) cell differentiation and organ primordia. The genes and gene components of this invention are useful for modulating any one or all of these cell division processes generally, as in timing and rate, for example. In addition, the polynucleotides and polypeptides of the invention can control the response of these processes to the internal plant programs associated with embryogenesis, and hormone responses, for example.

Because SAMs determine the architecture of the plant, modified plants are useful in many agricultural, horticultural, forestry and other industrial sectors. Plants with a different shape, numbers of flowers and seed and fruits have altered yields of plant parts. For example, plants with more branches produce more flowers, seed or fruits. Trees without lateral branches produce long lengths of clean timber. Plants with greater yields of specific plant parts are useful sources of constituent chemicals.

III.C. Hormone Responsive Genes, Gene Components and Products

III.C.1. Abscissic Acid Responsive Genes, Gene Components and Products

Plant hormones are naturally occurring substances, effective in very small amounts, which act as signals to stimulate or inhibit growth or regulate developmental processes in plants. Abscisic acid (ABA) is a ubiquitous hormone in vascular plants that has been detected in every major organ or living tissue from the root to the apical bud. The major physiological responses affected by ABA are dormancy, stress stomatal closure, water uptake, abscission and senescence. In contrast to Auxins, cytokinins and gibberellins, which are principally growth promoters, ABA primarily acts as an inhibitor of growth and metabolic processes.

Changes in ABA concentration internally or in the surrounding environment in contact with a plant results in modulation of many genes and gene products. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield.

While ABA responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different ABA responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of an ABA responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress and defence induced pathways, nutritional pathways and development.

III.C.2. Brassinosteroid Responsive Genes, Gene Components and Products:

Plant hormones are naturally occurring substances, effective in very small amounts, which act as signals to stimulate or inhibit growth or regulate developmental processes in plants. Brassinosteroids (BRs) are the most recently discovered, and least studied, class of plant hormones. The major physiological response affected by BRs is the longitudinal growth of young tissue via cell elongation and cell division. Consequently, disruptions in BR metabolism, perception and activity result in a dwarf phenotype. In addition, because BRs are derived from the sterol metabolic pathway, any perturbations to the sterol pathway affect the BR pathway. In the same way, perturbations in the BR pathway have effects on the later part of the sterol pathway and thus the sterol composition of membranes.

Changes in BR concentration in the surrounding environment or in contact with a plant result in modulation of many genes and gene products.

While BR responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different BR responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factors and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of a BR responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is useful because of the interactions that exist between hormone-regulated pathways, stress pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways.

III.C.3. Cytokinin Responsive Genes, Gene Components and Products

Plant hormones are naturally occurring substances, effective in very small amounts, which act as signals to stimulate or inhibit growth or regulate developmental processes in plants. Cytokinins (BA) are a group of hormones that are best known for their stimulatory effect on cell division, although they also participate in many other processes and pathways. All naturally occurring BAs are aminopurine derivatives, while nearly all synthetic compounds with BA activity are 6-substituted aminopurine derivatives. One of the most common synthetic BAs used in agriculture is benzylaminopurine (BAP).

BA responsive genes are useful to modulate plant growth, emergence of lateral buds, cotyledon expansion, senescence, differentiation, nutrient metabolism, control of fruit ripening, and parthenocarpy.

III.D. Metabolism Affecting Genes, Gene Components and Products

III.D.1. Nitrogen Responsive Genes, Gene Components and Products

Nitrogen is often the rate-limiting element in plant growth, and all field crops have a fundamental dependence on exogenous nitrogen sources. Nitrogenous fertilizer, which is usually supplied as ammonium nitrate, potassium nitrate, or urea, typically accounts for 40% of the costs associated with crops in intensive agriculture, such as corn and wheat. Increased efficiency of nitrogen use by plants enables the production of higher yields with existing fertilizer inputs and/or enable existing yields of crops to be obtained with lower fertilizer input, or better yields from growth on soils of poorer quality. Also, higher amounts of proteins in the crops are produced more cost-effectively. “Nitrogen responsive” genes and gene products are used to alter or modulate plant growth and development.

III.D.2. Blue Light (Phototropism) Responsive Genes, Gene Components and Products

Phototropism is the orientation or growth of a cell, an organism or part of an organism in relation to a source of light. Plants can sense red (R), far-red (FR) and blue light in their environment and respond differently to particular ratios of these. For example, a low R:FR ratio enhances cell elongation and favors flowering over leaf production, but blue light regulated cryptochromes also appear to be involved in determining hypocotyl growth and flowering time.

Phototropism of Arabidopsis thaliana seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a blue light-activated serine-threonine protein kinase, but the downstream signaling events are not entirely known. Blue light treatment leads to changes in gene expression. These genes are identified by comparing the levels of mRNAs of individual genes in dark-grown seedlings compared with dark grown seedlings treated with 1 hour of blue light.

Auxin also affects blue light phototropism. The effect of Auxin on gene expression stimulated by blue light is found by comparing mRNA levels in a mutant of Arabidopsis thaliana nph4-2 grown in the dark and treated with blue light for 1 hour with wild type seedlings treated similarly. This mutant is disrupted for Auxin-related growth and Auxin-induced gene transcription.

Blue light responsive genes are used to alter or modulate growth, roots (elongation or gravitropism), stems (such as elongation), cell development, flower, seedling, plant yield, and seed and fruit yield.

III.D.3 Carbon Dioxide Responsive Genes, Gene Components and Products

There has been a recent and significant increase in the level of atmospheric carbon dioxide. This rise in level is projected to continue over the next 50 years. The effects of the increased level of carbon dioxide on vegetation are just now being examined, generally in large scale, whole plant experiments often conducted with trees. Some researchers have initiated physiological experiments in attempts to define the biochemical pathways that are either affected by and/or are activated to allow the plant to avert damage from elevated carbon dioxide levels.

CO₂ responsive genes are useful to modulate catabolism, energy generation, metabolism, carbohydrate synthesis, growth rate and photosynthesis (such as carbon dioxide fixation).

III.D.4. Viability Genes, Gene Components and Products

Plants contain many proteins and pathways that when blocked or induced lead to cell, organ or whole plant death. Gene variants that influence these pathways have profound effects on plant survival, vigor and performance. The critical pathways include those concerned with metabolism and development or protection against stresses, diseases and pests. They also include those involved in apoptosis and necrosis. Viability genes are modulated to affect cell or plant death.

Herbicides are, by definition, chemicals that cause death of tissues, organs and whole plants. The genes and pathways that are activated or inactivated by herbicides include those that cause cell death as well as those that function to provide protection.

III.E. Stress Responsive Genes, Gene Components and Products

III.E.1. Cold Responsive Genes, Gene Components and Products

The ability to endure low temperatures and freezing is a major determinant of the geographical distribution and productivity of agricultural crops. Even areas considered suitable for the cultivation of a given species or cultivar can give rise to yield decreases and crop failures as a result of aberrant freezing temperatures. Even modest increases (1-2° C.) in the freezing tolerance of certain crop species have a dramatic impact on agricultural productivity in some areas. The development of genotypes with increased freezing tolerance provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the microclimate.

Sudden cold temperatures result in modulation of many genes and gene products. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield.

Manipulation of one or more cold responsive gene activities is useful to modulate growth and development.

III.E.2. Heat Responsive Genes, Gene Components and Products

The ability to endure high temperatures is a major determinant of the geographical distribution and productivity of agricultural crops. Decreases in yield and crop failure frequently occur as a result of aberrant hot conditions even in areas considered suitable for the cultivation of a given species or cultivar. Only modest increases in the heat tolerance of crop species have a dramatic impact on agricultural productivity. The development of genotypes with increased heat tolerance provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the microclimate.

III.E.3. Drought Responsive Genes, Gene Components and Products

The ability to endure drought conditions is a major determinant of the geographical distribution and productivity of agricultural crops. Decreases in yield and crop failure frequently occur as a result of aberrant drought conditions even in areas considered suitable for the cultivation of a given species or cultivar. Only modest increases in the drought tolerance of crop species have a dramatic impact on agricultural productivity. The development of genotypes with increased drought tolerance provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the microclimate.

III.E.4. Wounding Responsive Genes, Gene Components and Products

Plants are continuously subjected to various forms of wounding from physical attacks including the damage created by pathogens and pests, wind, and contact with other objects. Therefore, survival and agricultural yields depend on constraining the damage created by the wounding process and inducing defense mechanisms against future damage.

Plants have evolved complex systems to minimize and/or repair local damage and to minimize subsequent attacks by pathogens or pests or their effects. These involve stimulation of cell division and cell elongation to repair tissues, induction of programmed cell death to isolate damage caused mechanically and by invading pests and pathogens, and induction of long-range signaling systems to induce protecting molecules in case of future attack. The genetic and biochemical systems associated with responses to wounding are connected with those associated with other stresses such as pathogen attack and drought.

Wounding results in the modulation of activities of specific genes and, as a consequence, of the levels of key proteins and metabolites. These genes, called here wounding responsive genes, are important for minimizing the damage induced by wounding from pests, pathogens and other objects.

III.E.5. Methyl Jasmonate (Jasmonate) Responsive Genes, Gene Components and Products

Jasmonic acid and its derivatives, collectively referred to as jasmonates, are naturally occurring derivatives of plant lipids. These substances are synthesized from linolenic acid in a lipoxygenase-dependent biosynthetic pathway. Jasmonates are signalling molecules which are growth regulators as well as regulators of defense and stress responses. As such, jasmonates represent a separate class of plant hormones. Jasmonate responsive genes can be used to modulate plant growth and development.

III.E.6. Salicylic Acid Responsive Genes, Gene Components and Products

Plant defense responses can be divided into two groups: constitutive and induced. Salicylic acid (SA) is a signaling molecule necessary for activation of the plant induced defense system known as systemic acquired resistance or SAR. This response, which is triggered by prior exposure to avirulent pathogens, is long lasting and provides protection against a broad spectrum of pathogens. Another induced defense system is the hypersensitive response (HR). HR is far more rapid, occurs at the sites of pathogen (avirulent pathogens) entry and precedes SAR. SA is also the key signaling molecule for this defense pathway.

SA genes are useful to modulate plant defense systems.

III.E.7. Nitric Oxide Responsive Genes, Gene Components and Products

The rate-limiting element in plant growth and yield is often its ability to tolerate suboptimal or stress conditions, including pathogen attack conditions, wounding and the presence of various other factors. To combat such conditions, plant cells deploy a battery of inducible defense responses, including synergistic interactions between nitric oxide (NO), reactive oxygen intermediates (ROS), and salicylic acid (SA). NO plays a critical role in the activation of innate immune and inflammatory responses in animals. At least part of this mammalian signaling pathway is present in plants, where NO potentiates the hypersensitive response (HR). In addition, NO is a stimulator molecule in plant photomorphogenesis.

Changes in nitric oxide concentration in the internal or surrounding environment, or in contact with a plant, results in modulation of many genes and gene products.

In addition, the combination of a nitric oxide responsive polynucleotide and/or gene product with other environmentally responsive polynucleotides is also useful because of the interactions that exist between hormone regulated pathways, stress pathways, pathogen stimulated pathways, nutritional pathways and development.

Nitric oxide responsive genes and gene products function either to increase or dampen the above phenotypes or activities either in response to changes in nitric oxide concentration or in the absence of nitric oxide fluctuations. More specifically, these genes and gene products modulate stress responses in an organism. In plants, these genes and gene products are useful for modulating yield under stress conditions. Measurements of yield include seed yield, seed size, fruit yield, fruit size, etc.

III.E.8. Osmotic Stress Responsive Genes, Gene Components and Products

The ability to endure and recover from osmotic and salt related stress is a major determinant of the geographical distribution and productivity of agricultural crops. Osmotic stress is a major component of stress imposed by saline soil and water deficit. Decreases in yield and crop failure frequently occur as a result of aberrant or transient environmental stress conditions even in areas considered suitable for the cultivation of a given species or cultivar. Only modest increases in the osmotic and salt tolerance of a crop species have a dramatic impact on agricultural productivity. The development of genotypes with increased osmotic tolerance provides a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the soil environment. Thus, osmotic stress responsive genes are used to modulate plant growth and development.

III.E.9. Disease Responsive Genes, Gene Components and Products

Often growth and yield are limited by the ability of a plant to tolerate stress conditions, including pathogen attack. To combat such conditions, plant cells deploy a battery of inducible defense responses, including the triggering of an oxidative burst and the transcription of pathogenesis-related protein (PR protein) genes. These responses depend on the recognition of a microbial avirulence gene product (avr) by a plant resistance gene product (R), and a series of downstream signaling events leading to transcription-independent and transcription-dependent disease resistance responses. Reactive oxygen species (ROS) such as H₂O₂ and NO from the oxidative burst play a signaling role, including initiation of the hypersensitive response (HR) and induction of systemic acquired resistance (SAR) to secondary infection by unrelated pathogens. PR proteins are able to degrade the cell walls of invading microorganisms, and phytoalexins are directly microbicidal.

Disease responsive genes and gene products are useful to modulate plant response to pathogen attack including bacteria, fungi, virus, insects and nematodes.

III.E.10. Shade Responsive Genes, Gene Components and Products

Plants sense the ratio of Red (R): Far Red (FR) light in their environment and respond differently to particular ratios. A low R:FR ratio, for example, enhances cell elongation and favors flowering over leaf production. The changes in R:FR ratios mimic and cause the shading response effects in plants. The response of a plant to shade in the canopy structures of agricultural crop fields influences crop yields significantly. Therefore manipulation of genes regulating the shade avoidance responses can improve crop yields.

While phytochromes mediate the shade avoidance response, the down-stream factors participating in this pathway are largely unknown. One potential downstream participant, ATHB-2, is a member of the HD-Zip class of transcription factors and shows a strong and rapid response to changes in the R:FR ratio. ATHB-2 overexpressors have a thinner root mass, smaller and fewer leaves and longer hypocotyls and petioles. This elongation arises from longer epidermal and cortical cells, and a decrease in secondary vascular tissues, paralleling the changes observed in wild-type seedlings grown under conditions simulating canopy shade.

On the other hand, plants with reduced ATHB-2 expression have a thick root mass and many larger leaves and shorter hypocotyls and petioles. Here, the changes in the hypocotyl result from shorter epidermal and cortical cells and increased proliferation of vascular tissue. Interestingly, application of Auxin is able to reverse the root phenotypic consequences of high ATHB-2 levels, restoring the wild-type phenotype. Consequently, given that ATHB-2 is tightly regulated by phytochrome, these data indicate that ATHB-2 links the Auxin and phytochrome pathways in the shade avoidance response pathway.

Shade responsive genes can be used to modulate plant growth and development.

III.E.11 Guard Cell Genes, Gene Components and Products

Scattered throughout the epidermis of the shoot are minute pores called stomata. Each stomal pore is surrounded by two guard cells. The guard cells control the size of the stomal pore, which is critical since the stomata control the exchange of carbon dioxide, oxygen, and water vapor between the interior of the plant and the outside atmosphere. Stomata open and close through turgor changes driven by ion fluxes, which occur mainly through the guard cell plasma membrane and tonoplast. Guard cells are known to respond to a number of external stimuli such as changes in light intensity, carbon dioxide and water vapor, for example. Guard cells can also sense and rapidly respond to internal stimuli including changes in ABA, auxin and calcium ion flux.

Thus, guard cell genes are useful to modulate ABA responses, drought tolerance, respiration, water potential, and water management. All of which in turn affect plant yield including seed yield, harvest index, fruit yield, etc.

IV. Enhanced Foods

Animals require external supplies of amino acids that they cannot synthesize themselves. Also, some amino acids are required in larger quantities. The nutritional values of plants for animals and humans are thus modified by regulating the amounts of the constituent amino acids that occur as free amino acids or in proteins. For instance, higher levels of lysine and/or methionine enhance the nutritional value of corn seed. Applicants herein provide several methods for modulating the amino acid content:

-   -   (1) expressing a naturally occurring protein that has a high         percentage of the desired amino acid(s);     -   (2) expressing a modified or synthetic coding sequence that has         an enhanced percentage of the desired amino acids; or     -   (3) expressing the protein(s) that are capable of synthesizing         more of the desired amino acids.         A specific example is expressing proteins with, for example,         enhanced methionine content, preferentially in a corn or cereal         seed used for animal nutrition or in the parts of plants used         for nutritional purposes.

A protein is considered to have a high percentage of an amino acid if the amount of the desired amino acid is at least 1% of the total number of residues in a protein; more preferably 2% or greater. Amino acids of particular interest are tryptophan, lysine, methionine, phenylalanine, threonine leucine, valine, and isoleucine.

The sequence(s) encoding the selected protein(s) is operably linked to a promoter and other regulatory sequences and transformed into a plant as described below. The promoter is chosen for promoting the optimal desired level of expression of the protein in the selected organ e.g. a promoter highly functional in seeds. Modifications may be made to the sequence encoding the protein to ensure protein transport into, for example, organelles or storage bodies or its accumulation in the organ. Such modifications may include addition of signal sequences at or near the N terminus and amino acid residues to modify protein stability or appropriate glycosylation. Other modifications may be made to the transcribed nucleic acid sequence to enhance the stability or translatability of the mRNA, in order to ensure accumulation of more of the desired protein. Suitable versions of the gene construct and transgenic plants are selected on the basis of, for example, the improved amino acid content and nutritional value measured by standard biochemical tests and animal feeding trials.

V. Use of Novel Genes to Facilitate Exploitation of Plants as Factories for the Synthesis of Valuable Molecules

Plants and their constituent cells, tissues, and organs are factories that manufacture small organic molecules such as sugars, amino acids, fatty acids, vitamins, etc., as well as macromolecules such as proteins, nucleic acids, oils/fats and carbohydrates. Plants have long been a source of pharmaceutically beneficial chemical, particularly the secondary metabolites and hormone-related molecules synthesized by plants. Plants can also be used as factories to produce carbohydrates or lipids that comprises a carbon backbone useful as the precursor of plastics, fiber, fuel, paper, pulp, rubber, solvents, lubricants, construction materials, detergents, and other cleaning materials. Plants can also generate other compounds that are of economic value, such as dyes, flavors and fragrances. Both the intermediates as well as the end-products of plant bio-synthetic pathways have been found useful.

With the polynucleotides and polypeptides of the instant invention, modification of both in-vitro and in-vivo synthesis of such products is possible. One method of increasing the amount of either the intermediates or the end-products synthesized in a cell is to increase the expression of one or more proteins in the synthesis pathway as discussed below. Another method of increasing production of an intermediate is to inhibit expression of protein(s) that synthesize the end-product from the intermediate. Levels of end-products and intermediates are also modified by changing the levels of enzymes that specifically change or degrade them. The kinds of molecules made are also modified by changing the genes encoding specific enzymes performing reactions at specific steps of the biosynthetic pathway. These genes are from the same or a different organism. The molecular structures in the biosynthetic pathways is thus modified or diverted into different branches of a pathway to make novel end-products.

The modifications are made by designing one or more novel genes per application comprising promoters, to ensure production of the enzyme(s) in the relevant cells, in the right amount, and polynucleotides encoding the relevant enzyme. The promoters and polynucleotides are the subject of this application. The novel genes are transformed into the relevant species using standard procedures. Their effects are measured by standard assays for the specific chemical/biochemical products.

The polynucleotides and proteins of the invention that participate in the relevant pathways and are useful for changing production of the above chemicals and biochemicals are identified in the Reference tables by their enzyme function. More specifically, proteins of the invention that have the enzymatic activity of one of the entries in the following table entitled “Enzymes Effecting Modulation of Biological Pathways” are of interest to modulate the corresponding pathways to produce precursors or final products noted above that are of industrial use. Biological activities of particular interest are listed below.

Other polynucleotides and proteins that regulate where, when and to what extent a pathway is active in a plant are extremely useful for modulating the synthesis and accumulation of valuable chemicals. These elements include transcription factors, proteins involved in signal transduction and other proteins in the control of gene expression and are described elsewhere in this application.

Pathway Name Enzyme Description Comments Alkaloid biosynthesis I Morphine 6- Also acts on other alkaloids, including dehydrogenase codeine, normorphine and ethylmorphine, but only very slowly on 7,8-saturated derivatives such as dihydromorphine and dihydrocodeine In the reverse direction, also reduces naloxone to the 6-alpha- hydroxy analog Activated by 2- mercaptoethanol Codeinone reductase Stereospecifically catalyses the reversible (NADPH) reduction of codeinone to codeine, which is a direct precursor of morphine in the opium poppy plant, Papaver somniferum Salutaridine reductase Stereospecifically catalyses the reversible (NADPH) reduction of salutaridine to salutaridinol, which is a direct precursor of morphinan alkaloids in the poppy plant, Papaver somniferum (S)-stylopine synthase Catalyses an oxidative reaction that does not incorporate oxygen into the product Forms the second methylenedioxy bridge of the protoberberine alkaloid stylopine from oxidative ring closure of adjacent phenolic and methoxy groups of cheilanthifoline (S)-cheilanthifoline Catalyses an oxidative reaction that does synthase not incorporate oxygen into the product Forms the methylenedioxy bridge of the protoberberine alkaloid cheilanthifoline from oxidative ring closure of adjacent phenolic and methoxy groups of scoulerine Salutaridine synthase Forms the morphinan alkaloid salutaridine by intramolecular phenol oxidation of reticuline without the incorporation of oxygen into the product (S)-canadine synthase Catalyses an oxidative reaction that does not incorporate oxygen into the product Oxidation of the methoxyphenol group of the alkaloid tetrahydrocolumbamine results in the formation of the methylenedioxy bridge of canadine Protopine 6- Involved in benzophenanthridine alkaloid monooxygenase synthesis in higher plants Dihydrosanguinarine Involved in benzophenanthridine alkaloid 10-monooxygenase synthesis in higher plants Monophenol A group of copper proteins that also monooxygenase catalyse the reaction of EC 1.10.3.1, if only 1,2-benzenediols are available as substrate L-amino acid oxidase 1,2- Stereospecifically reduces the 1,2- dehydroreticulinium dehydroreticulinium ion to (R)-reticuline, reductase (NADPH) which is a direct precursor of morphinan alkaloids in the poppy plant, papaver somniferum The enzyme does not catalyse the reverse reaction to any significant extent under physiological conditions Dihydrobenzo- Also catalyzes: dihydrochelirubine + O(2) = phenanthridine oxidase chelirubine + H(2)O(2) Also catalyzes: dihydromacarpine + O(2) = macarpine + H(2)O(2) Found in higher plants Produces oxidized forms of the benzophenanthridine alkaloids Reticuline oxidase The product of the reaction, (S)- scoulerine, is a precursor of protopine, protoberberine and benzophenanthridine alkaloid biosynthesis in plants Acts on (S)-reticuline and related compounds, converting the N-methyl group into the methylene bridge (′berberine bridge[PRIME]) of (S)- tetrahydroprotoberberines 3[PRIME]-hydroxy-N- Involved in isoquinoline alkaloid methyl-(S)-coclaurine metabolism in plants Has also been shown 4[PRIME]-O- to catalyse the methylation of (R,S)- methyltransferase laudanosoline, (S)-3[PRIME]- hydroxycoclaurine and (R,S)-7-O- methylnoraudanosoline (S)-scoulerine 9-O- The product of this reaction is a precursor methyltransferase for protoberberine alkaloids in plants Columbamine O- The product of this reaction is a methyltransferase protoberberine alkaloid that is widely distributed in the plant kingdom Distinct in specificity from EC 2.1.1.88 10-hydroxydihydro- Part of the pathway for synthesis of sanguinarine 10-O- benzophenanthridine alkaloids in plants methyltransferase 12-hydroxydi- Part of the pathway for synthesis of hydrochelirubine 12-O- benzophenanthridine alkaloid macarpine methyltransferase in plants (R,S)-norcoclaurine 6- Norcoclaurine is 6,7-dihydroxy-1-[(4- O-methyltransferase hydroxyphenyl)methyl]-1,2,3,4- tetrahydroisoquinoline The enzyme will also catalyse the 6-O-methylation of (R,S)-norlaudanosoline to form 6-O- methyl-norlaudanosoline, but this alkaloid has not been found to occur in plants Salutaridinol 7-O- At higher pH values the product, 7-O- acetyltransferase acetylsalutaridinol, spontaneously closes the 4->5 oxide bridge by allylic elimination to form the morphine precursor thebaine From the opium poppy plant, Papaver somniferum Aspartate Also acts on L-tyrosine, L-phenylalanine aminotransferase and L-tryptophan. This activity can be formed from EC 2.6.1.57 by controlled proteolysis Tyrosine L-phenylalanine can act instead of L- aminotransferase tyrosine The mitochondrial enzyme may be identical with EC 2.6.1.1 The three isoenzymic forms are interconverted by EC 3.4.22.4 Aromatic amino acid L-methionine can also act as donor, more transferase slowly Oxaloacetate can act as acceptor Controlled proteolysis converts the enzyme to EC 2.6.1.1 Tyrosine decarboxylase The bacterial enzyme also acts on 3- hydroxytyrosine and, more slowly, on 3- hydroxyphenylalanine Aromatic-L-amino-acid Also acts on L-tryptophan, 5-hydroxy-L- decarboxylase tryptophan and dihydroxy-L- phenylalanine (DOPA) Alkaloid biosynthesis II Tropine dehydrogenase Oxidizes other tropan-3-alpha-ols, but not the corresponding beta-derivatives Tropinone reductase Hyoscyamine (6S)- dioxygenase 6-beta- hydroxyhyoscyamine epoxidase Amine oxidase (copper- A group of enzymes including those containing) oxidizing primary amines, diamines and histamine One form of EC 1.3.1.15 from rat kidney also catalyses this reaction Putrescine N- methyltransferase Ornithine decarboxylase Oxalyl-CoA decarboxylase Phenylalanine May also act on L-tyrosine ammonia-lyase Androgen and estrogen 3-beta-hydroxy- Acts on 3-beta-hydroxyandrost-5-en-17- metabolism delta(5)-steroid one to form androst-4-ene-3,17-dione and dehydrogenase on 3-beta-hydroxypregn-5-en-20-one to form progesterone 11-beta-hydroxysteroid dehydrogenase Estradiol 17-alpha- dehydrogenase 3-alpha-hydroxy-5- beta-androstane-17-one 3-alpha-dehydrogenase 3-alpha (17-beta)- Also acts on other 17-beta- hydroxysteroid hydroxysteroids, on the 3-alpha-hydroxy dehydrogenase (NAD+) group of pregnanes and bile acids, and on benzene dihydrodiol Different from EC 1.1.1.50 or EC 1.1.1.213 3-alpha-hydroxysteroid Acts on other 3-alpha-hydroxysteroids dehydrogenase (B- and on 9-, 11- and 15- specific) hydroxyprostaglandin B-specific with respect to NAD(+) or NADP(+) (cf. EC 1.1.1.213) 3(or 17)beta- Also acts on other 3-beta- or 17-beta- hydroxysteroid hydroxysteroids (cf EC 1.1.1.209) dehydrogenase Estradiol 17 beta- Also acts on (S)-20-hydroxypregn-4-en-3- dehydrogenase one and related compounds, oxidizing the (S)-20-group B-specific with respect to NAD(P)(+) Testosterone 17-beta- dehydrogenase Testosterone 17-beta- Also oxidizes 3-hydroxyhexobarbital to 3- dehydrogenase oxohexobarbital (NADP+) Steroid 11-beta- Also hydroxylates steroids at the 18- monooxygenase position, and converts 18- hydroxycorticosterone into aldosterone Estradiol 6-beta- monooxygenase Androst-4-ene-3,17- Has a wide specificity A single enzyme dione monooxygenase from Cylindrocarpon radicicola (EC 1.14.13.54) catalyses both this reaction and that catalysed by EC 1.14.99.4 3-oxo-5-alpha-steroid 4-dehydrogenase 3-oxo-5-beta-steroid 4- dehydrogenase UDP- Family of enzymes accepting a wide glucuronosyltransferase range of substrates, including phenols, alcohols, amines and fatty acids Some of the activities catalysed were previously listed separately as EC 2.4.1.42, EC 2.4.1.59, EC 2.4.1.61, EC 2.4.1.76, EC 2.4.1.77, EC 2.4.1.84, EC 2.4.1.107 and EC 2.4.1.108 A temporary nomenclature for the various forms whose delineation is in a state of flux Steroid sulfotransferase Broad specificity resembling EC 2.8.2.2, but also acts on estrone Alcohol Primary and secondary alcohols, sulfotransferase including aliphatic alcohols, ascorbate, chloramphenicol, ephedrine and hydroxysteroids, but not phenolic steroids, can act as acceptors (cf. EC 2.8.2.15) Estrone sulfotransferase Arylsulfatase A group of enzymes with rather similar specificities Steryl-sulfatase Also acts on some related steryl sulfates 17-alpha- hydroxyprogesterone aldolase Steroid delta-isomerase C21-Steroid hormone 3-beta-hydroxy- Acts on 3-beta-hydroxyandrost-5-en-17- metabolism delta(5)-steroid one to form androst-4-ene-3,17-dione and dehydrogenase on 3-beta-hydroxypregn-5-en-20-one to form progesterone 11-beta-hydroxysteroid dehydrogenase 20-alpha- A-specific with respect to NAD(P)(+) hydroxysteroid dehydrogenase 3-alpha-hydroxysteroid Acts on other 3-alpha-hydroxysteroids dehydrogenase (B- and on 9-, 11- and 15- specific) hydroxyprostaglandin B-specific with respect to NAD(+) or NADP(+) (cf. EC 1.1.1.213) 3-alpha(or 20-beta)- The 3-alpha-hydroxyl group or 20-beta- hydroxysteroid hydroxyl group of pregnane and dehydrogenase androstane steroids can act as donors Steroid 11-beta- Also hydroxylates steroids at the 18- monooxygenase position, and converts 18- hydroxycorticosterone into aldosterone Corticosterone 18- monooxygenase Cholesterol The reaction proceeds in three stages, monooxygenase (side- with hydroxylation at C-20 and C-22 chain cleaving) preceding scission of the side-chain at C- 20 Steroid 21- monooxygenase Progesterone 11-alpha- monooxygenase Steroid 17-alpha- monooxygenase Cholestenone 5-beta- reductase Cortisone beta- reductase Progesterone 5-alpha- Testosterone and 20-alpha-hydroxy-4- reductase pregnen-3-one can act in place of progesterone 3-oxo-5-beta-steroid 4- dehydrogenase Steroid delta-isomerase Flavonoids, stilbene and Coniferyl-alcohol Specific for coniferyl alcohol; does not lignin biosynthesis dehydrogenase act on cinnamyl alcohol, 4-coumaryl alcohol or sinapyl alcohol Cinnamyl-alcohol Acts on coniferyl alcohol, sinapyl alcohol, dehydrogenase 4-coumaryl alcohol and cinnamyl alcohol (cf. EC 1.1.1.194) Dihydrokaempferol 4- Also acts, in the reverse direction, on (+)- reductase dihydroquercetin and (+)- dihydromyricetin Each dihydroflavonol is reduced to the corresponding cis-flavon- 3,4-diol NAD(+) can act instead of NADP(+), more slowly Involved in the biosynthesis of anthocyanidins in plants Flavonone 4-reductase Involved in the biosynthesis of 3- deoxyanthocyanidins from flavonones such as naringenin or eriodictyol Peroxidase Caffeate 3,4- dioxygenase Naringenin 3- dioxygenase Trans-cinnamate 4- Also acts on NADH, more slowly monooxygenase Trans-cinnamate 2- monooxygenase Flavonoid 3[PRIME]- Acts on a number of flavonoids, including monooxygenase naringenin and dihydrokaempferol Does not act on 4-coumarate or 4-coumaroyl- CoA Monophenol A group of copper proteins that also monooxygenase catalyse the reaction of EC 1.10.3.1, if only 1,2-benzenediols are available as substrate Cinnamoyl-CoA Also acts on a number of substituted reductase cinnamoyl esters of coenzyme A Caffeoyl-CoA O- methyltransferase Luteolin O- Also acts on luteolin-7-O-beta-D- methyltransferase glucoside Caffeate O- 3,4-dihydroxybenzaldehyde and catechol methyltransferase can act as acceptor, more slowly Apigenin 4[PRIME]-O- Converts apigenin into acacetin methyltransferase Naringenin (5,7,4[PRIME]- trihydroxyflavonone) can also act as acceptor, more slowly Quercetin 3-O- Specific for quercetin. Related enzymes methyltransferase bring about the 3-O-methylation of other flavonols, such as galangin and kaempferol Isoflavone-7-O-beta- The 6-position of the glucose residue of glucoside formononetin can also act as acceptor 6[PRIME][PRIME]-O- Some other 7-O-glucosides of malonyltransferase isoflavones, flavones and flavonols can also act, more slowly Pinosylvin synthase Not identical with EC 2.3.1.74 or EC 2.3.1.95 Naringenin-chalcone In the presence of NADH and a reductase, synthase 6[PRIME]-deoxychalcone is produced Trihydroxystilbene Not identical with EC 2.3.1.74 or EC synthase 2.3.1.146 Quinate O- Caffeoyl-CoA and 4-coumaroyl-CoA can hydroxycinnamoyltransferase also act as donors, more slowly Involved in the biosynthesis of chlorogenic acid in sweet potato and, with EC 2.3.1.98 in the formation of caffeoyl-CoA in tomato Coniferyl-alcohol Sinapyl alcohol can also act as acceptor glucosyltransferase 2-coumarate O-beta- Coumarinate (cis-2-hydroxycinnamate) glucosyltransferase does not act as acceptor Scopoletin glucosyltransferase Flavonol-3-O-glucoside Converts flavonol 3-O-glucosides to 3-O- L-rhamnosyltransferase rutinosides Also acts, more slowly, on rutin, quercetin 3-O-galactoside and flavonol O3-rhamnosides Flavone 7-O-beta- A number of flavones, flavonones and glucosyltransferase flavonols can function as acceptors Different from EC 2.4.1.91 Flavonol 3-O- Acts on a variety of flavonols, including glucosyltransferase quercetin and quercetin 7-O-glucoside Different from EC 2.4.1.81 Flavone 7-O-beta-D-glucosides of a number of apiosyltransferase flavonoids and of 4-substituted phenols can act as acceptors Coniferin beta- Also hydrolyzes syringin, 4-cinnamyl glucosidase alcohol beta-glucoside, and, more slowly, some other aryl beta-glycosides A plant cell-wall enzyme involved in the biosynthesis of lignin Beta-glucosidase Wide specificity for beta-D-glucosides. Some examples also hydrolyse one or more of the following: beta-D- galactosides, alpha-L-arabinosides, beta- D-xylosides, and beta-D-fucosides Chalcone isomerase 4-coumarate--CoA ligase Ascorbate and aldarate D-threo-aldose 1- Acts on L-fucose, D-arabinose and L- metabolism dehydrogenase xylose The animal enzyme was also shown to act on L-arabinose, and the enzyme from Pseudomonas caryophylli on L-glucose L-threonate 3- dehydrogenase Glucuronate reductase Also reduces D-galacturonate May be identical with EC 1.1.1.2 Glucuronolactone reductase L-arabinose 1- dehydrogenase L-galactonolactone Acts on the 1,4-lactones of L-galactonic, oxidase D-altronic, L-fuconic, D-arabinic and D- threonic acids Not identical with EC 1.1.3.8 (cf. EC 1.3.2.3) L-gulonolactone The product spontaneously isomerizes to oxidase L-ascorbate L-ascorbate oxidase L-ascorbate peroxidase Ascorbate 2,3- dioxygenase 2,5-dioxovalerate dehydrogenase Aldehyde Wide specificity, including oxidation of dehydrogenase (NAD+) D-glucuronolactone to D-glucarate Galactonolactone Cf. EC 1.1.3.24 dehydrogenase Monodehydroascorbate reductase (NADH) Glutathione dehydrogenase (ascorbate) L-arabinonolactonase Gluconolactonase Acts on a wide range of hexono-1,5- lactones Uronolactonase 1,4-lactonase Specific for 1,4-lactones with 4-8 carbon atoms Does not hydrolyse simple aliphatic esters, acetylcholine, sugar lactones or substituted aliphatic lactones, e.g. 3-hydroxy-4-butyrolactone 2-dehydro-3- deoxyglucarate aldolase L-arabinonate dehydratase Glucarate dehydratase 5-dehydro-4- deoxyglucarate dehydratase Galactarate dehydratase 2-dehydro-3-deoxy-L- arabinonate dehydratase Carbon fixation Malate dehydrogenase Also oxidizes some other 2- hydroxydicarboxylic acids Malate dehydrogenase Does not decarboxylates added (decarboxylating) oxaloacetate Malate dehydrogenase Also decarboxylates added oxaloacetate (oxaloacetate decarboxylating) (NADP+) Malate dehydrogenase Activated by light (NADP+) Glyceraldehyde-3- phosphate dehydrogenase (NADP+) (phosphorylating) Transketolase Wide specificity for both reactants, e.g. converts hydroxypyruvate and R—CHO into CO(2) and R—CHOH—CO—CH(2)OH Transketolase from Alcaligenes faecalis shows high activity with D-erythrose as acceptor Aspartate Also acts on L-tyrosine, L-phenylalanine aminotransferase and L-tryptophan. This activity can be formed from EC 2.6.1.57 by controlled proteolysis Alanine 2-aminobutanoate acts slowly instead of aminotransferase alanine Sedoheptulokinase Phosphoribulokinase Pyruvate kinase UTP, GTP, CTP, ITP and dATP can also act as donors Also phosphorylates hydroxylamine and fluoride in the presence of CO(2) Phosphoglycerate kinase Pyruvate, phosphate dikinase Fructose- The animal enzyme also acts on bisphosphatase sedoheptulose 1,7-bisphosphate Sedoheptulose- bisphosphatase Phosphoenolpyruvate carboxylase Ribulose-bisphosphate Will utilize O(2) instead of CO(2), carboxylase forming 3-phospho-D-glycerate and 2- phosphoglycolate Phosphoenolpyruvate carboxykinase (ATP) Fructose-bisphosphate Also acts on (3S,4R)-ketose 1-phosphates aldolase The yeast and bacterial enzymes are zinc proteins The enzymes increase electron- attraction by the carbonyl group, some (Class I) forming a protonated imine with it, others (Class II), mainly of microbial origin, polarizing it with a metal ion, e.g zinc Phosphoketolase Ribulose-phosphate 3- Also converts D-erythrose 4-phosphate epimerase into D-erythrulose 4-phosphate and D- threose 4-phosphate Triosephosphate isomerase Ribose 5-phosphate Also acts on D-ribose 5-diphosphate and epimerase D-ribose 5-triphosphate Phenylalanine (R)-4- Also acts, more slowly, on (R)-3- metabolism hydroxyphenyllactate phenyllactate, (R)-3-(indole-3-yl)lactate dehydrogenase and (R)-lactate Hydroxyphenyl- Also acts on 3-(3,4- pyruvate reductase dihydroxyphenyl)lactate Involved with EC 2.3.1.140 in the biosynthesis of rosmarinic acid Aryl-alcohol A group of enzymes with broad dehydrogenase specificity towards primary alcohols with an aromatic or cyclohex-1-ene ring, but with low or no activity towards short- chain aliphatic alcohols Peroxidase Catechol 1,2- Involved in the metabolism of nitro- dioxygenase aromatic compounds by a strain of Pseudomonas putida 2,3-dihydroxybenzoate 3,4-dioxygenase 3-carboxyethylcatechol 2,3-dioxygenase Catechol 2,3- The enzyme from Alcaligines sp. strain dioxygenase O-1 has also been shown to catalyse the reaction: 3-Sulfocatechol + O(2) + H(2)O = 2-hydroxymuconate + bisulfite. It has been referred to as 3-sulfocatechol 2,3- dioxygenase. Further work will be necessary to show whether or not this is a distinct enzyme 4- hydroxyphenylpyruvate dioxygenase Protocatechuate 3,4- dioxygenase Hydroxyquinol 1,2- The product isomerizes to 2- dioxygenase maleylacetate (cis-hex-2-enedioate) Highly specific; catechol and pyrogallol are acted on at less than 1% of the rate at which benzene-1,2,4-triol is oxidized Protocatechuate 4,5- dioxygenase Phenylalanine 2- Also catalyses a reaction similar to that monooxygenase of EC 1.4.3.2, forming 3-phenylpyruvate, NH(3) and H(2)O(2), but more slowly Anthranilate 1,2- dioxygenase (deaminating, decarboxylating) Benzoate 1,2- A system, containing a reductase which dioxygenase is an iron-sulfur flavoprotein (FAD), and an iron-sulfur oxygenase Toluene dioxygenase A system, containing a reductase which is an iron-sulfur flavoprotein (FAD), an iron-sulfur oxygenase, and a ferredoxin Some other aromatic compounds, including ethylbenzene, 4-xylene and some halogenated toluenes, are converted into the corresponding cis-dihydrodiols Naphthalene 1,2- A system, containing a reductase which dioxygenase is an iron-sulfur flavoprotein (FAD), an iron-sulfur oxygenase, and ferredoxin Benzene 1,2- A system, containing a reductase which dioxygenase is an iron-sulfur flavoprotein, an iron- sulfur oxygenase and ferredoxin Salicylate 1- monooxygenase Trans-cinnamate 4- Also acts on NADH, more slowly monooxygenase Benzoate 4- monooxygenase 4-hydroxybenzoate 3- Most enzymes from Pseudomonas are monooxygenase highly specific for NAD(P)H (cf EC 1.14.13.33) 3-hydroxybenzoate 4- Also acts on a number of analogs of 3- monooxygenase hydroxybenzoate substituted in the 2, 4, 5 and 6 positions 3-hydroxybenzoate 6- Also acts on a number of analogs of 3- monooxygenase hydroxybenzoate substituted in the 2, 4, 5 and 6 positions NADPH can act instead of NADH, more slowly 4-hydroxybenzoate 3- The enzyme from Corynebacterium monooxygenase cyclohexanicum is highly specific for 4- (NAD(P)H) hydroxybenzoate, but uses NADH and NADPH at approximately equal rates (cf. EC 1.14.13.2). It is less specific for NADPH than EC 1.14.13.2 Anthranilate 3- The enzyme from Aspergillus niger is an monooxygenase iron protein; that from the yeast (deaminating) Trichosporon cutaneum is a flavoprotein (FAD) Melilotate 3- monooxygenase Phenol 2- Also active with resorcinol and O-cresol monooxygenase Mandelate 4- monooxygenase 3-hydroxybenzoate 2- monooxygenase 4-cresol dehydrogenase Phenazine methosulfate can act as (hydroxylating) acceptor A quinone methide is probably formed as intermediate The product is oxidized further to 4-hydroxybenzoate Benzaldehyde dehydrogenase (NAD+) Aminomuconate- Also acts on 2-hydroxymuconate semialdehyde semialdehyde dehydrogenase Phenylacetaldehyde dehydrogenase 4-carboxy-2- Does not act on unsubstituted aliphatic or hydroxymuconate-6- aromatic aldehydes or glucose NAD(+) semialdehyde can replace NADP(+), but with lower dehydrogenase affinity Aldehyde dehydrogenase (NAD(P)+) Benzaldehyde dehydrogenase (NADP+) Coumarate reductase Cis-1,2- dihydrobenzene-1,2- diol dehydrogenase Cis-1,2-dihydro-1,2- Also acts, at half the rate, on cis- dihydroxynaphthalene anthracene dihydrodiol and cis- dehydrogenase phenanthrene dihydrodiol 2-enoate reductase Acts, in the reverse direction, on a wide range of alkyl and aryl alpha,beta- unsaturated carboxylate ions 2-butenoate was the best substrate tested Maleylacetate reductase Phenylalanine The enzyme from Bacillus badius and dehydrogenase Sporosarcina ureae are highly specific for L-phenylalanine, that from Bacillus sphaericus also acts on L-tyrosine L-amino acid oxidase Amine oxidase (flavin- Acts on primary amines, and usually also containing) on secondary and tertiary amines Amine oxidase (copper- A group of enzymes including those containing) oxidizing primary amines, diamines and histamine One form of EC 1.3.1.15 from rat kidney also catalyses this reaction D-amino-acid Acts to some extent on all D-amino acids dehydrogenase except D-aspartate and D-glutamate Aralkylamine Phenazine methosulfate can act as dehydrogenase acceptor Acts on aromatic amines and, more slowly, on some long-chain aliphatic amines, but not on methylamine or ethylamine (cf EC 1.4.99.3) Glutamine N- phenylacetyltrans- ferase Acetyl-CoA C- acyltransferase D-amino-acid N- acetyltransferase Phenylalanine N- Also acts, more slowly, on L-histidine acetyltransferase and L-alanine Glycine N- Not identical with EC 2.3.1.13 or EC benzoyltransferase 2.3.1.68 Aspartate Also acts on L-tyrosine, L-phenylalanine aminotransferase and L-tryptophan. This activity can be formed from EC 2.6.1.57 by controlled proteolysis D-alanine Acts on the D-isomers of leucine, aminotransferase aspartate, glutamate, aminobutyrate, norvaline and asparagine Tyrosine L-phenylalanine can act instead of L- aminotransferase tyrosine The mitochondrial enzyme may be identical with EC 2.6.1.1 The three isoenzymic forms are interconverted by EC 3.4.22.4 Aromatic amino acid L-methionine can also act as donor, more transferase slowly Oxaloacetate can act as acceptor Controlled proteolysis converts the enzyme to EC 2.6.1.1 Histidinol-phosphate aminotransferase 3-oxoadipate CoA- transferase 3-oxoadipate enol- Acts on the product of EC 4.1.1.44 lactonase Carboxymethylene- butenolidase 2-pyrone-4,6- The product isomerizes to 4- dicarboxylate lactonase oxalmesaconate Hippurate hydrolase Acts on various N-benzoylamino acids Amidase Acylphosphatase 2-hydroxymuconate- semialdehyde hydrolase Aromatic-L-amino-acid Also acts on L-tryptophan, 5-hydroxy-L- decarboxylase tryptophan and dihydroxy-L- phenylalanine (DOPA) Phenylpyruvate Also acts on indole-3-pyruvate decarboxylase 4-carboxymucono- lactone decarboxylase O-pyrocatechuate decarboxylase Phenylalanine Also acts on tyrosine and other aromatic decarboxylase amino acids 4-hydroxybenzoate decarboxylase Protocatechuate decarboxylase Benzoylformate decarboxylase 4-oxalocrotonate Involved in the meta-cleavage pathway decarboxylase for the degradation of phenols, cresols and catechols 4-hydroxy-4-methyl-2- Also acts on 4-hydroxy-4-methyl-2- oxoglutarate aldolase oxoadipate and 4-carboxy-4-hydroxy-2- oxohexadioate 2-oxopent-4-enoate Also acts, more slowly, on cis-2-oxohex- hydratase 4-enoate, but not on the trans-isomer Phenylalanine May also act on L-tyrosine ammonia-lyase Phenylalanine racemase (ATP-hydrolysing) Mandelate racemase Phenylpyruvate Also acts on other arylpyruvates tautomerase 5-carboxymethyl-2- hydroxymuconate delta-isomerase Muconolactone delta- isomerase Muconate Also acts, in the reverse reaction, on 3- cycloisomerase methyl-cis-cis-hexa-dienedioate and, very slowly, on cis-trans-hexadienedioate Not identical with EC 5.5.1.7 or EC 5.5.1.11 3-carboxy-cis,cis- muconate cycloisomerase Carboxy-cis,cis- muconate cyclase Chloromuconate Spontaneous elimination of HCl produces cycloisomerase cis-4-carboxymethylenebut-2-en-4-olide Also acts in reverse direction on 2- chloro-cis,cis-muconate Not identical with EC 5.5.1.1 or EC 5.5.1.11 Phenylacetate--CoA Phenoxyacetate can replace phenylacetate ligase Benzoate--CoA ligase Also acts on 2-, 3- and 4-fluorobenzoate, but only very slowly on the corresponding chlorobenzoates 4-hydroxybenzoate-- CoA ligase Phenylacetate--CoA Also acts, more slowly, on acetate, ligase propanoate and butanoate, but not on hydroxy derivatives of phenylacetate and related compounds Phenylalanine, tyrosine Quinate 5- and tryptophan biosynthesis dehydrogenase Shikimate 5- dehydrogenase Quinate dehydrogenase (pyrroloquinoline- quinone) Phenylalanine 4- monooxygenase Prephenate This enzyme in the enteric bacteria also dehydrogenase possesses chorismate mutase activity (EC 5.4.99.5) and converts chorismate into prephenate Prephenate dehydrogenase (NADP+) Cyclohexadienyl Also acts on prephenate and D- dehydrogenase prephenyllactate (cf. EC 1.3.1.12) 2-methyl-branched- From Ascaris suum The reaction chain-enoyl-CoA proceeds only in the presence of another reductase flavoprotein (ETF = [PRIME]Electron- Transferring Flavoprotein[PRIME]) Phenylalanine The enzyme from Bacillus badius and dehydrogenase Sporosarcina ureae are highly specific for L-phenylalanine, that from Bacillus sphaericus also acts on L-tyrosine L-amino acid oxidase Anthranilate In some organisms, this enzyme is part of phosphoribosyl- a multifunctional protein together with transferase one or more components of the system for biosynthesis of tryptophan (EC 4.1.1.48, EC 4.1.3.27, EC 4.2.1.20, and EC 5.3.1.24) 3-phosphoshikimate 1- carboxyvinyl- transferase Aspartate Also acts on L-tyrosine, L-phenylalanine aminotransferase and L-tryptophan. This activity can be formed from EC 2.6.1.57 by controlled proteolysis Tyrosine L-phenylalanine can act instead of L- aminotransferase tyrosine The mitochondrial enzyme may be identical with EC 2.6.1.1 The three isoenzymic forms are interconverted by EC 3.4.22.4 Aromatic amino acid L-methionine can also act as donor, more transferase slowly Oxaloacetate can act as acceptor Controlled proteolysis converts the enzyme to EC 2.6.1.1 Histidinol-phosphate aminotransferase Shikimate kinase Indole-3-glycerol- In some organisms, this enzyme is part of phosphate synthase a multifunctional protein together with one or more components of the system for biosynthesis of tryptophan (EC 2.4.2.18, EC 4.1.3.27, EC 4.2.1.20, and EC 5.3.1.24) 2-dehydro-3- deoxyphosphoheptonate aldolase Anthranilate synthase In some organisms, this enzyme is part of a multifunctional protein together with one or more components of the system for biosynthesis of tryptophan (EC 2.4.2.18, EC 4.1.1.48, EC 4.2.1.20, and EC 5.3.1.24) The native enzyme in the complex with uses either glutamine or (less efficiently) NH(3). The enzyme separated from the complex uses NH(3) only 3-dehydroquinate dehydratase Phosphopyruvate Also acts on 3-phospho-D-erythronate hydratase Tryptophan synthase Also catalyses the conversion of serine and indole into tryptophan and water and of indoleglycerol phosphate into indole and glyceraldehyde phosphate In some organisms, this enzyme is part of a multifunctional protein together with one or more components of the system for biosynthesis of tryptophan (EC 2.4.2.18, EC 4.1.1.48, EC 4.1.3.27, and EC 5.3.1.24) Prephenate dehydratase This enzyme in the enteric bacteria also possesses chorismate mutase activity and converts chorismate into prephenate Carboxycyclohexadienyl Also acts on prephenate and D- dehydratase prephenyllactate Cf. EC 4.2.1.51 3-dehydroquinate The hydrogen atoms on C-7 of the synthase substrate are retained on C-2 of the products Chorismate synthase Shikimate is numbered so that the double-bond is between C-1 and C-2, but some earlier papers numbered in the reverse direction Phosphoribosylanthranilate In some organisms, this enzyme is part of isomerase a multifunctional protein together with one or more components of the system for biosynthesis of tryptophan (EC 2.4.2.18, EC 4.1.1.48, EC 4.1.3.27, and EC 4.2.1.20) Chorismate mutase Tyrosine--tRNA ligase Phenylalanine--tRNA ligase Starch and sucrose UDP-glucose 6- Also acts on UDP-2-deoxyglucose metabolism dehydrogenase Glucoside 3- The enzyme acts on D-glucose, D- dehydrogenase galactose, D-glucosides and D- galactosides, but D-glucosides react more rapidly than D-galactosides CDP-4-dehydro-6- Two proteins are involved but no partial deoxyglucose reductase reaction has been observed in the presence of either alone Phosphorylase The recommended name should be qualified in each instance by adding the name of the natural substance, e.g. maltodextrin phosphorylase, starch phosphorylase, glycogen phosphorylase Levansucrase Some other sugars can act as D-fructosyl acceptors Glycogen (starch) The recommended name varies according synthase to the source of the enzyme and the nature of its synthetic product Glycogen synthase from animal tissues is a complex of a catalytic subunit and the protein glycogenin The enzyme requires glucosylated glycogenin as a primer; this is the reaction product of EC 2.4.1.186 A similar enzyme utilizes ADP-glucose (Cf. EC 2.4.1.21) Cellulose synthase Involved in the synthesis of cellulose A (UDP-forming) similar enzyme utilizes GDP-glucose (Cf. EC 2.4.1.29) Sucrose synthase Sucrose-phosphate synthase Alpha, alpha-trehalose- See also EC 2.4.1.36 phosphate synthase (UDP-forming) UDP- Family of enzymes accepting a wide glucuronosyltransferase range of substrates, including phenols, alcohols, amines and fatty acids Some of the activities catalysed were previously listed separately as EC 2.4.1.42, EC 2.4.1.59, EC 2.4.1.61, EC 2.4.1.76, EC 2.4.1.77, EC 2.4.1.84, EC 2.4.1.107 and EC 2.4.1.108 A temporary nomenclature for the various forms whose delineation is in a state of flux 1,4-alpha-glucan Converts amylose into amylopectin The branching enzyme recommended name requires a qualification depending on the product, glycogen or amylopectin, e.g. glycogen branching enzyme, amylopectin branching enzyme. The latter has frequently been termed Q-enzyme Cellobiose phosphorylase Starch (bacterial The recommended name various glycogen) synthase according to the source of the enzyme and the nature of its synthetic product, e.g. starch synthase, bacterial glycogen synthase A similar enzyme utilizes UDP- glucose (Cf. EC 2.4.1.11) 4-alpha- An enzymic activity of this nature forms glucanotransferase part of the mammalian and Yeast glycogen branching system (see EC 3.2.1.33) Cellulose synthase Involved in the synthesis of cellulose A (GDP-forming) similar enzyme utilizes UDP-glucose (Cf. EC 2.4.1.12) 1,3-beta-glucan synthase Phenol beta- Acts on a wide range of phenols glucosyltransferase Amylosucrase Polygalacturonate 4- alpha- galacturonosyltransferase Dextransucrase Alpha,alpha-trehalose phosphorylase Sucrose phosphorylase In the forward reaction, arsenate may replace phosphate In the reverse reaction various ketoses and L-arabinose may replace D-fructose Maltose phosphorylase 1,4-beta-D-xylan synthase Hexokinase D-glucose, D-mannose, D-fructose, sorbitol and D-glucosamine can act as acceptors ITP and dATP can act as donors The liver isoenzyme has sometimes been called glucokinase Phosphoglucokinase Glucose-1,6- D-glucose 6-phosphate can act as bisphosphate synthase acceptor, forming D-glucose 1,6- bisphosphate Glucokinase A group of enzymes found in invertebrates and microorganisms highly specific for glucose Fructokinase Glucose-1-phosphate phosphodismutase Protein-N(PI)- Comprises a group of related enzymes phosphohistidine-sugar The protein substrate is a phosphocarrier phosphotransferase protein of low molecular mass (9.5 Kd) A phosphoenzyme intermediate is formed The enzyme translocates the sugar it phosphorylates into bacteria Aldohexoses and their glycosides and alditols are phosphorylated on O-6; fructose and sorbose on O-1 Glycerol and disaccharides are also substrates Glucose-1-phosphate adenylyltransferase Glucose-1-phosphate cytidylyltransferase Glucose-1-phosphate Also acts, more slowly, on D-mannose 1- guanylyltransferase phosphate UTP--glucose-1- phosphate uridylyltransferase Pectinesterase Trehalose-phosphatase Sucrose-phosphatase Glucose-6-phosphatase Wide distribution in animal tissues Also catalyses potent transphosphorylations from carbamoyl phosphate, hexose phosphates, pyrophosphate, phosphoenolpyruvate and nucleoside di- and triphosphates, to D-glucose, D- mannose, 3-methyl-D-glucose, or 2- deoxy-D-glucose (cf. EC 2.7.1.62, EC 2.7.1.79, and EC 3.9.1.1) Alpha-amylase Acts on starch, glycogen and related polysaccharides and oligosaccharides in a random manner; reducing groups are liberated in the alpha-configuration Oligo-1,6-glucosidase Also hydrolyses palatinose The enzyme from intestinal mucosa is a single polypeptide chain also catalysing the reaction of EC 3.2.1.48 Maltose-6[PRIME]- Hydrolyses a variety of 6-phospho-D- phosphate glucosidase glucosides, including maltose 6- phosphate, alpha[PRIME] alpha-trehalose 6-phosphate, sucrose 6-phosphate and p- nitrophenyl-alpha-D-glucopyranoside 6- phosphate (as a chromogenic substrate) The enzyme is activated by Fe(II), Mn(II), Co(II) and Ni(II). It is rapidly inactivated in air Polygalacturonase Beta-amylase Acts on starch, glycogen and related polysaccharides and oligosaccharides producing beta-maltose by an inversion Alpha-glucosidase Group of enzymes whose specificity is directed mainly towards the exohydrolysis of 1,4-alpha-glucosidic linkages, and that hydrolyse oligosaccharides rapidly, relative to polysaccharides, which are hydrolysed relatively slowly, or not at all The intestinal enzyme also hydrolyses polysaccharides, catalysing the reactions of EC 3.2.1.3, and, more slowly, hydrolyses 1,6-alpha-D-glucose links Beta-glucosidase Wide specificity for beta-D-glucosides. Some examples also hydrolyse one or more of the following: beta-D- galactosides, alpha-L-arabinosides, beta- D-xylosides, and beta-D-fucosides Beta-fructofuranosidase Substrates include sucrose Also catalyses fructotransferase reactions Alpha,alpha-trehalase Glucan 1,4-alpha- Most forms of the enzyme can rapidly glucosidase hydrolyse 1,6-alpha-D-glucosidic bonds when the next bond in sequence is 1,4, and some preparations of this enzyme hydrolyse 1,6- and 1,3-alpha-D- glucosidic bonds in other polysaccharides This entry covers all such enzymes acting on polysaccharides more rapidly than on oligosaccharides EC 3.2.1.20 from mammalian intestine can catalyse similar reactions Beta-glucuronidase Amylo-1,6-glucosidase In mammals and yeast this enzyme is linked to a glycosyltransferase similar to EC 2.4.1.25; together these two activities constitute the glycogen debranching system Xylan 1,4-beta- Also hydrolyses xylobiose Some other xylosidase exoglycosidase activities have been found associated with this enzyme in sheep liver Glucan endo-1,3-beta- Very limited action on mixed-link (1,3- D-glucosidase 1,4-)-beta-D-glucans Hydrolyses laminarin, paramylon and pachyman Different from EC 3.2.1.6 Cellulase Will also hydrolyse 1,4-linkages in beta- D-glucans also containing 1,3-linkages Sucrose alpha- This enzyme is isolated from intestinal glucosidase mucosa as a single polypeptide chain also displaying activity towards isomaltose (oligo-1,6-glucosidase, cf. EC 3.2.1.10) Cyclomaltodextrinase Also hydrolyses linear maltodextrin Glucan 1,3-beta- Acts on oligosaccharides but very slowly glucosidase on laminaribiose Levanase Galacturan 1,4-alpha- galacturonidase Glucan 1,4-beta- Acts on 1,4-beta-D-glucans and related glucosidase oligosaccharides Cellobiose is hydrolysed, very slowly Cellulose 1,4-beta- cellobiosidase Alpha,alpha- phosphotrehalase ADP-sugar Has a distinct specificity from the UDP- diphosphatase sugar pyrophosphatase (EC 3.6.1.45) Nucleotide Substrates include NAD(+), NADP(+), pyrophosphatase FAD, CoA and also ATP and ADP UDP-glucuronate decarboxylase CDP-glucose 4,6- dehydratase CDP-abequose epimerase UDP-glucuronate 4- epimerase Glucose-6-phosphate Also catalyses the anomerization of D- isomerase glucose 6-phosphate Phosphoglucomutase Maximum activity is only obtained in the presence of alpha-D-glucose 1,6- bisphosphate. This bisphosphate is an intermediate in the reaction, being formed by transfer of a phosphate residue from the enzyme to the substrate, but the dissociation of bisphosphate from the enzyme complex is much slower than the overall isomerization Also, more slowly, catalyses the interconversion of 1- phosphate and 6-phosphate isomers of many other alpha-D-hexoses, and the interconversion of alpha-D-ribose 1- phosphate and 5-phosphate Beta- phosphoglucomutase Maltose alpha-D- glucosyltransferase Tryptophan metabolism Indole-3-lactate dehydrogenase Indole-3-acetaldehyde reductase (NADH) Indole-3-acetaldehyde reductase (NADPH) 3-hydroxyacyl-CoA Also oxidizes S-3-hydroxyacyl-N- dehydrogenase acylthioethanolamine and S-3- hydroxyacylhydrolipoate Some enzymes act, more slowly, with NADP(+) Broad specificity to acyl chain-length (cf. EC 1.1.1.211) O-aminophenol oxidase Isophenoxazine may be formed by a secondary condensation from the initial oxidation product Catalase This enzyme can also act as a peroxidase (EC 1.11.1.7) for which several organic substances, especially ethanol, can act as a hydrogen donor A manganese protein containing Mn(III) in the resting state, which also belongs here, is often called pseudocatalase Enzymes from some microorganisms, such as Penicillium simplicissimum, which exhibit both catalase and peroxidase activity, have sometimes been referred to as catalase- peroxidase 7,8- dihydroxykynurenate 8,8A-dioxygenase Tryptophan 2,3- Broad specificity towards tryptamine and dioxygenase derivatives including D- and L- tryptophan, 5-hydroxytryptophan and serotonin Indole 2,3-dioxygenase The enzyme from jasminum is a flavoprotein containing copper, and forms anthranilate as the final product One enzyme from Tecoma stans is also a flavoprotein containing copper and uses three atoms of oxygen per molecule of Indole, to form anthranil (3,4- benzisoxazole) A second enzyme from Tecoma stans, which is not a flavoprotein, uses four atoms of oxygen and forms anthranilate as the final product 2,3-dihydroxyindole 2,3-dioxygenase Indoleamine-pyrrole Acts on many substituted and 2,3-dioxygenase unsubstituted indoleamines, including melatonin Involved in the degradation of melatonin 3-hydroxyanthranilate The product of the reaction 3,4-dioxygenase spontaneously rearrange to quinolinic acid (quin) Tryptophan 2- monooxygenase Tryptophan 2[PRIME]- Acts on a number of indolyl-3-alkane dioxygenase derivatives, oxidizing the 3-side-chain in the 2[PRIME]-position. Best substrates are L-tryptophan and 5-hydroxy-L- tryptophan Kynurenine 3- monooxygenase Unspecific Acts on a wide range of substrates monooxygenase including many xenobiotics, steroids, fatty acids, vitamins and prostaglandins Reactions catalysed include hydroxylation, epoxidation, N-oxidation, sulfooxidation, N-, S- and O- dealkylations, desulfation, deamination, and reduction of azo, nitro, and N-oxide groups Anthranilate 3- monooxygenase Tryptophan 5- Activated by phosphorylation, catalysed monooxygenase by a CA(2+)-activated protein kinase Kynurenine 7,8- hydroxylase Aldehyde Wide specificity, including oxidation of dehydrogenase (NAD+) D-glucuronolactone to D-glucarate Aminomuconate- Also acts on 2-hydroxymuconate semialdehyde semialdehyde dehydrogenase Aldehyde oxidase Also oxidizes quinoline and pyridine derivatives May be identical with EC 1.1.3.22 Indole-3-acetaldehyde Also oxidizes indole-3-aldehyde and oxidase acetaldehyde, more slowly Oxoglutarate Component of the multienzyme 2- dehydrogenase oxoglutarate dehydrogenase complex (lipoamide) Kynurenate-7,8- dihydrodiol dehydrogenase Glutaryl-CoA dehydrogenase L-amino acid oxidase Amine oxidase (flavin- Acts on primary amines, and usually also containing) on secondary and tertiary amines Amine oxidase (copper- A group of enzymes including those containing) oxidizing primary amines, diamines and histamine One form of EC 1.3.1.15 from rat kidney also catalyses this reaction Acetylindoxyl oxidase Acetylserotonin O- Some other hydroxyindoles also act as methyltransferase acceptor, more slowly Indole-3-pyruvate C- methyltransferase Amine N- A wide range of primary, secondary, and methyltransferase tertiary amines can act as acceptors, including tryptamine, aniline, nicotine and a variety of drugs and other xenobiotics Aralkylamine N- Narrow specificity towards acetyltransferase aralkylamines, including serotonin Not identical with EC 2.3.1.5 Acetyl-CoA C- acetyltransferase Tryptophan Also acts on 5-hydroxytryptophan and, to aminotransferase a lesser extent on the phenyl amino acids Kynurenine-- Also acts on 3-hydroxykynurenine oxoglutarate aminotransferase Thioglucosidase Has a wide specificity for thioglycosides Amidase Formamidase Also acts, more slowly, on acetamide, propanamide and butanamide Arylformamidase Also acts on other aromatic formylamines Nitrilase Acts on a wide range of aromatic nitriles including (indole-3-yl)-acetonitrile and also on some aliphatic nitriles, and on the corresponding acid amides (cf. EC 4.2.1.84) Kynureninase Also acts on 3[PRIME]- hydroxykynurenine and some other (3- arylcarbonyl)-alanines Aromatic-L-amino-acid Also acts on L-tryptophan, 5-hydroxy-L- decarboxylase tryptophan and dihydroxy-L- phenylalanine (DOPA) Phenylpyruvate Also acts on indole-3-pyruvate decarboxylase Aminocarboxymuconate- The product rearranges non-enzymically semialdehyde to picolinate decarboxylase Tryptophanase Also catalyses the synthesis of tryptophan from indole and serine Also catalyses 2,3-elimination and beta- replacement reactions of some indole- substituted tryptophan analogs of L- cysteine, L-serine and other 3-substituted amino acids Enoyl-CoA hydratase Acts in the reverse direction With cis- compounds, yields (3R)-3-hydroxyacyl- CoA (cf. EC 4.2.1.74) Nitrile hydratase Acts on short-chain aliphatic nitriles, converting them into the corresponding acid amides Does not act on these amides or on aromatic nitriles (cf EC 3.5.5.1) Tryptophan--tRNA ligase Tyrosine metabolism Alcohol dehydrogenase Acts on primary or secondary alcohols or hemiacetals The animal, but not the yeast, enzyme acts also on cyclic secondary alcohols (R)-4- Also acts, more slowly, on (R)-3- hydroxyphenyllactate phenyllactate, (R)-3-(indole-3-yl)lactate dehydrogenase and (R)-lactate Hydroxyphenylpyruvate Also acts on 3-(3,4- reductase dihydroxyphenyl)lactate Involved with EC 2.3.1.140 in the biosynthesis of rosmarinic acid Aryl-alcohol A group of enzymes with broad dehydrogenase specificity towards primary alcohols with an aromatic or cyclohex-1-ene ring, but with low or no activity towards short- chain aliphatic alcohols Catechol oxidase Also acts on a variety of substituted catechols Many of these enzymes also catalyse the reaction listed under EC 1.14.18.1; this is especially true for the classical tyrosinase Iodide peroxidase 3,4- dihydroxyphenylacetate 2,3-dioxygenase 4- hydroxyphenylpyruvate dioxygenase Stizolobate synthase The intermediate product undergoes ring closure and oxidation, with NAD(P)(+) as acceptor, to stizolobic acid Stizolobinate synthase The intermediate product undergoes ring closure and oxidation, with NAD(P)(+) as acceptor, to stizolobinic acid Gentisate 1,2- dioxygenase Homogentisate 1,2- dioxygenase 4-hydroxyphenylacetate Also acts on 4-hydroxyhydratropate 1-monooxygenase forming 2-methylhomogentisate and on 4-hydroxyphenoxyacetate forming hydroquinone and glycolate 4-hydroxyphenylacetate 3-monooxygenase Tyrosine N- monooxygenase Hydroxyphenylacetonitrile 2-monooxygenase Tyrosine 3- Activated by phosphorylation, catalysed monooxygenase by EC 2.7.1.128 Dopamine-beta- Stimulated by fumarate monooxygenase Monophenol A group of copper proteins that also monooxygenase catalyse the reaction of EC 1.10.3.1, if only 1,2-benzenediols are available as substrate Succinate- semialdehyde dehydrogenase (NAD(P)+) Aryl-aldehyde Oxidizes a number of aromatic dehydrogenase aldehydes, but not aliphatic aldehydes Aldehyde Wide specificity, including oxidation of dehydrogenase (NAD+) D-glucuronolactone to D-glucarate 4-carboxy-2- Does not act on unsubstituted aliphatic or hydroxymuconate-6- aromatic aldehydes or glucose NAD(+) semialdehyde can replace NADP(+), but with lower dehydrogenase affinity Aldehyde dehydrogenase (NAD(P)+) 4- With EC 4.2.1.87, brings about the hydroxyphenylacetalde metabolism of octopamine in hyde dehydrogenase Pseudomonas Aldehyde oxidase Also oxidizes quinoline and pyridine derivatives May be identical with EC 1.1.3.22 L-amino acid oxidase Amine oxidase (flavin- Acts on primary amines, and usually also containing) on secondary and tertiary amines Amine oxidase (copper- A group of enzymes including those containing) oxidizing primary amines, diamines and histamine One form of EC 1.3.1.15 from rat kidney also catalyses this reaction Aralkylamine Phenazine methosulfate can act as dehydrogenase acceptor Acts on aromatic amines and, more slowly, on some long-chain aliphatic amines, but not on methylamine or ethylamine (cf EC 1.4.99.3) Phenol O- Acts on a wide variety of simple alkyl-, methyltransferase methoxy- and halo-phenols Tyramine N- Has some activity on phenylethylamine methyltransferase analogs Phenylethanolamine N- Acts on various phenylethanolamines; methyltransferase converts noradrenalin into adrenalin Catechol O- The mammalian enzymes act more methyltransferase rapidly on catecholamines such as adrenaline or noradrenaline than on catechols Glutamine N- phenylacetyltransferase Rosmarinate synthase Involved with EC 1.1.1.237 in the biosynthesis of rosmarinic acid Hydroxymandelonitrile 3,4-dihydroxymandelonitrile can also act glucosyltransferase as acceptor Aspartate Also acts on L-tyrosine, L-phenylalanine aminotransferase and L-tryptophan. This activity can be formed from EC 2.6.1.57 by controlled proteolysis Dihydroxyphenylalanine aminotransferase Tyrosine L-phenylalanine can act instead of L- aminotransferase tyrosine The mitochondrial enzyme may be identical with EC 2.6.1.1 The three isoenzymic forms are interconverted by EC 3.4.22.4 Aromatic amino acid L-methionine can also act as donor, more transferase slowly Oxaloacetate can act as acceptor Controlled proteolysis converts the enzyme to EC 2.6.1.1 Histidinol-phosphate aminotransferase Fumarylacetoacetase Also acts on other 3,5- and 2,4-dioxo acids Acylpyruvate hydrolase Acts on formylpyruvate, 2,4- dioxopentanoate, 2,4-dioxohexanoate and 2,4-dioxoheptanoate Tyrosine decarboxylase The bacterial enzyme also acts on 3- hydroxytyrosine and, more slowly, on 3- hydroxyphenylalanine Aromatic-L-amino-acid Also acts on L-tryptophan, 5-hydroxy-L- decarboxylase tryptophan and dihydroxy-L- phenylalanine (DOPA) Gentisate decarboxylase 5-oxopent-3-ene-1,2,5- tricarboxylate decarboxylase Tyrosine phenol-lyase Also slowly catalyses pyruvate formation from D-tyrosine, S-methyl-L-cysteine, L-cysteine, L-serine and D-serine (S)-norcoclaurine The reaction makes a 6-membered ring synthase by forming a bond between C-6 of the 3,4-dihydroxyphenyl group of the dopamine and C-1 of the aldehyde in the imine formed between the substrates The product is the precursor of the benzylisoquinoline alkaloids in plants Will also catalyse the reaction of 4-(2- aminoethyl)benzene-1,2-diol + (3,4- dihydroxyphenyl)acetaldehyde to form (S)-norlaudanosoline, but this alkaloid has not been found to occur in plants Dihydroxyphenylalanine ammonia-lyase Phenylalanine May also act on L-tyrosine ammonia-lyase Maleylacetoacetate Also acts on maleylpyruvate isomerase Maleylpyruvate isomerase Phenylpyruvate Also acts on other arylpyruvates tautomerase 5-carboxymethyl-2- hydroxymuconate delta-isomerase Tyrosine 2,3- aminomutase Phenylacetate--CoA Also acts, more slowly, on acetate, ligase propanoate and butanoate, but not on hydroxy derivatives of phenylacetate and related compounds

VI. How to Make Different Embodiments of the Invention

The invention relates to (I) polynucleotides and methods of use thereof, such as

IA. Probes, Primers and Substrates;

IB. Methods of Detection and Isolation;

-   -   B.1. Hybridization;     -   B.2. Methods of Mapping;     -   B.3. Southern Blotting;     -   B.4. Isolating cDNA from Related Organisms;     -   B.5. Isolating and/or Identifying Orthologous Genes

IC. Methods of Inhibiting Gene Expression

-   -   C.1. Antisense     -   C.2. Ribozyme Constructs;     -   C.3. Chimeraplasts;     -   C.4 Sense Suppression;     -   C.5. Transcriptional Silencing     -   C.6. Other Methods to Inhibit Gene Expression

ID. Methods of Functional Analysis;

IE. UTRs and Junctions

IF. Coding Sequences and Their Use.

The invention also relates to (II) polypeptides and proteins and methods of use thereof, such as

IIA. Native Polypeptides and Proteins

-   -   A.1 Antibodies     -   A.2 In Vitro Applications

IIB. Polypeptide Variants, Fragments and Fusions

-   -   B.1 Variants     -   B.2 Fragments     -   B.3 Fusions

The invention also includes (III) methods of modulating polypeptide production, such as

IIIA. Suppression

-   -   A.1 Antisense     -   A.2 Ribozymes     -   A.3 Sense Suppression     -   A.4 Insertion of Sequences into the Gene to be Modulated     -   A.5 Promoter Modulation     -   A.6 Expression of Genes containing Dominant-Negative Mutations

IIIB. Enhanced Expression

-   -   B.1 Insertion of an Exogenous Gene     -   B.2 Promoter Modulation

The invention further concerns (IV) gene constructs and vector construction, such as

IVA. Coding Sequences

IVB. Promoters

IVC. Signal Peptides

The invention still further relates to

V. Transformation Techniques

I. Polynucleotides

Exemplified SDFs of the invention represent fragments of the genome of corn, wheat, rice, soybean or Arabidopsis and/or represent mRNA expressed from that genome. The isolated nucleic acid of the invention also encompasses corresponding fragments of the genome and/or cDNA complement of other organisms as described in detail below.

Polynucleotides of the invention are isolated from polynucleotide libraries using primers comprising sequences similar to those described, in the attached Reference and Sequences Tables or complements thereof. See, for example, the methods described in Sambrook et al., supra.

Alternatively, the polynucleotides of the invention can be produced by chemical synthesis. Such synthesis methods are described below.

It is contemplated that the nucleotide sequences presented herein contain some small percentage of errors. These errors arise in the normal course of determination of nucleotide sequences. Sequence errors can be corrected by obtaining seeds deposited under the accession numbers cited above, propagating them, isolating genomic DNA or appropriate mRNA from the resulting plants or seeds thereof, amplifying the relevant fragment of the genomic DNA or mRNA using primers having a sequence that flanks the erroneous sequence and sequencing the amplification product.

I.A. Probes, Primers and Substrates

SDFs of the invention can be applied to substrates for use in array applications such as, but not limited to, assays of global gene expression, under varying conditions of development, and growth conditions. The arrays are also used in diagnostic or forensic methods (WO95/35505, U.S. Pat. No. 5,445,943 and U.S. Pat. No. 5,410,270).

Probes and primers of the instant invention hybridize to a polynucleotide comprising a sequence in or encoded by those in the Reference and Sequence Tables or fragments or complements thereof. Though many different nucleotide sequences can encode an amino acid sequence, the sequences of the Reference and Sequence Table are generally preferred for encoding polypeptides of the invention. However, the sequence of the probes and/or primers of the instant invention need not be identical to those in the Reference and Sequence Tables or the complements thereof. For example, some variation in probe or primer sequence and/or length allows detection of additional family members as well as orthologous genes and more taxonomically distant related sequences. Similarly, probes and/or primers of the invention include additional nucleotides that serve as a label for detecting the formed duplex or for subsequent cloning purposes.

Probe length varys depending on the application. For use as primers, probes are 12-40 nucleotides, preferably 18-30 nucleotides long. For use in mapping, probes are preferably 50 to 500 nucleotides, preferably 100-250 nucleotides long. For Southern hybridizations, probes as long as several kilobases are used as explained below.

The probes and/or primers are produced by synthetic procedures such as the triester method of Matteucci et al. J. Am. Chem. Soc. 103:3185 (1981) or according to Urdea et al. Proc. Natl. Acad. 80:7461 (1981) or using commercially available automated oligonucleotide synthesizers.

I.B. Methods of Detection and Isolation

The polynucleotides of the invention can be utilized in a number of methods known to those skilled in the art as probes and/or primers to isolate and detect polynucleotides including, without limitation: Southerns, Northerns, Branched DNA hybridization assays, polymerase chain reaction microarray assays and variations thereof. Specific methods given by way of examples, and discussed below include:

Hybridization

Methods of Mapping

Southern Blotting

Isolating cDNA from Related Organisms

Isolating and/or Identifying Orthologous Genes.

Also, the nucleic acid molecules of the invention can used in other methods, such as high density oligonucleotide hybridizing assays, described, for example, in U.S. Pat. Nos. 6,004,753; 5,945,306; 5,945,287; 5,945,308; 5,919,686; 5,919,661; 5,919,627; 5,874,248; 5,871,973; 5,871,971; 5,871,930; and PCT Pub. Nos. WO 9946380; WO 9933981; WO 9933870; WO 9931252; WO 9915658; WO 9906572; WO 9858052; WO 9958672; and WO 9810858.

B.1. Hybridization

The isolated SDFs of the Reference and Sequence tables or fragments thereof of the present invention can be used as probes and/or primers for detection and/or isolation of related polynucleotide sequences through hybridization. Hybridization of one nucleic acid to another constitutes a physical property that defines the subject SDF of the invention and the identified related sequences. Also, such hybridization imposes structural limitations on the pair. A good general discussion of the factors for determining hybridization conditions is provided by Sambrook et al. (“Molecular Cloning, a Laboratory Manual, 2^(nd) ed., c. 1989 by Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; see esp., chapters 11 and 12). Additional considerations and details of the physical chemistry of hybridization are provided by G. H. Keller and M. M. Manak “DNA Probes”, 2^(nd) Ed. pp. 1-25, c. 1993 by Stockton Press, New York, N.Y.

Depending on the stringency of the conditions under which these probes and/or primers are used, polynucleotides exhibiting a wide range of similarity to those in the Reference and Sequence or fragments thereof are detected or isolated. When the practitioner wishes to examine the result of membrane hybridizations under a variety of stringencies, an efficient way to do so is to perform the hybridization under a low stringency condition, then to wash the hybridization membrane under increasingly stringent conditions.

When using SDFs to identify orthologous genes in other species, the practitioner will preferably adjust the amount of target DNA of each species so that, as nearly as is practical, the same number of genome equivalents are present for each species examined. This prevents faint signals from species having large genomes, and thus small numbers of genome equivalents per mass of DNA, from erroneously being interpreted as absence of the corresponding gene in the genome.

The probes and/or primers of the instant invention can also be used to detect or isolate nucleotides that are “identical” to the probes or primers. Two nucleic acid sequences or polypeptides are said to be “identical” if the sequence of nucleotides or amino acid residues, respectively, in the two sequences is the same when aligned for maximum correspondence as described below.

Isolated polynucleotides within the scope of the invention also include allelic variants of the specific sequences presented in the Reference and Sequence tables. The probes and/or primers of the invention are also used to detect and/or isolate polynucleotides exhibiting at least 80% sequence identity with the sequences of the Reference and Sequence tables or fragments thereof.

With respect to nucleotide sequences, degeneracy of the genetic code provides the possibility to substitute at least one nucleotide of the nucleotide sequence of a gene with a different nucleotide without changing the amino acid sequence of the polypeptide. Hence, the DNA of the present invention also has any base sequence that has been changed from a sequence in the Reference and Sequence tables by substitution in accordance with degeneracy of genetic code. References describing codon usage include: Carels et al., J. Mol. Evol. 46: 45 (1998) and Fennoy et al., Nucl. Acids Res. 21(23): 5294 (1993).

B.2. Mapping

The isolated SDF DNA of the invention is used to create various types of genetic and physical maps of the genome of corn, Arabidopsis, soybean, rice, wheat, or other plants. Some SDFs are absolutely associated with particular phenotypic traits, allowing construction of gross genetic maps. While not all SDFs are immediately associated with a phenotype, all SDFs can be used as probes for identifying polymorphisms associated with phenotypes of interest. Briefly, one method of mapping involves total DNA isolation from individuals. The DNA is subsequently cleaved with one or more restriction enzymes, separated according to mass, transferred to a solid support, hybridized with SDF DNA and the pattern of fragments compared. Polymorphisms associated with a particular SDF are visualized as differences in the size of fragments produced between individual DNA samples after digestion with a particular restriction enzyme and hybridization with the SDF. After identification of polymorphic SDF sequences, linkage studies are conducted. By using the polymeric individuals as parents in crossing programs, F2 progeny recombinants or recombinant inbreds, for example, are then analyzed. The order of DNA polymorphisms along the chromosomes is determined based on the frequency with which they are inherited together versus independently. The closer the location of two polymorphisms on a chromosome, the higher the probability that they are inherited together. Integration of the relative positions of all the polymorphisms and associated marker SDFs produce a genetic map of the species where the distances between markers reflect the recombination frequencies in that chromosome segment.

The use of recombinant inbred lines for such genetic mapping is described for Arabidopsis by Alonso-Blanco et al. (Methods in Molecular Biology, vol. 82, “Arabidopsis Protocols”, pp. 137-146, J. M. Martinez-Zapater and J. Salinas, eds., c. 1998 by Humana Press, Totowa, N.J.) and for corn by Burr (“Mapping Genes with Recombinant Inbreds”, pp. 249-254. In Freeling, M. and V. Walbot (Ed.), The Maize Handbook, c. 1994 by Springer-Verlag New York, Inc.: New York, N.Y., USA; Berlin Germany; Burr et al. Genetics (1998) 118: 519; Gardiner, J. et al., (1993) Genetics 134: 917). This procedure, however, is not limited to plants and is used for other organisms (such as yeast) or for individual cells.

The SDFs of the present invention are also used for simple sequence repeat (SSR) mapping. Rice SSR mapping is described by Morgante et al. (The Plant Journal (1993) 3: 165), Panaud et al. (Genome (1995) 38: 1170); Senior et al. (Crop Science (1996) 36: 1676), Taramino et al. (Genome (1996) 39: 277) and Ahn et al. (Molecular and General Genetics (1993) 241: 483-90). SSR mapping is achieved using various methods. In one instance, polymorphisms are identified when sequence specific probes contained within an SDF flanking an SSR are made and used in polymerase chain reaction (PCR) assays with template DNA from two or more individuals of interest. Here, a change in the number of tandem repeats between the SSR-flanking sequences produces differently sized fragments (U.S. Pat. No. 5,766,847). Alternatively, polymorphisms are identified by using the PCR fragment produced from the SSR-flanking sequence specific primer reaction as a probe against Southern blots representing different individuals (U. H. Refseth et al., (1997) Electrophoresis 18: 1519).

Genetic and physical maps of crop species have many uses. For example, these maps are used to devise positional cloning strategies for isolating novel genes from the mapped crop species. In addition, because the genomes of closely related species are largely syntenic (i.e. they display the same ordering of genes within the genome), these maps are used to isolate novel alleles from relatives of crop species by positional cloning strategies.

The various types of maps discussed above are used with the SDFs of the invention to identify Quantitative Trait Loci (QTLs). Many important crop traits, such as the solids content of tomatoes, are quantitative traits and result from the combined interactions of several genes. These genes reside at different loci in the genome, often times on different chromosomes, and generally exhibit multiple alleles at each locus. The SDFs of the invention are used to identify QTLs and isolate specific alleles as described by de Vicente and Tanksley (Genetics 134:585 (1993)). In addition to isolating QTL alleles in present crop species, the SDFs of the invention are also used to isolate alleles from the corresponding QTL of wild relatives. Transgenic plants having various combinations of QTL alleles are then created and the effects of the combinations measured. Once a desired allele combination is identified, crop improvement is accomplished either through biotechnological means or by directed conventional breeding programs (for review see Tanksley and McCouch, Science 277:1063 (1997)).

In another embodiment, the SDFs are used to help create physical maps of the genome of corn, Arabidopsis and related species. Where SDFs are ordered on a genetic map, as described above, they are used as probes to discover which clones in large libraries of plant DNA fragments in YACs, BACs, etc. contain the same SDF or similar sequences, thereby facilitating the assignment of the large DNA fragments to chromosomal positions. Subsequently, the large BACs, YACs, etc. are ordered unambiguously by more detailed studies of their sequence composition (e.g. Marra et al. (1997) Genomic Research 7:1072-1084) and by using their end or other sequences to find the identical sequences in other cloned DNA fragments. The overlapping of DNA sequences in this way allows building large contigs of plant sequences to be built that, when sufficiently extended, provide a complete physical map of a chromosome. Sometimes the SDFs themselves provide the means of joining cloned sequences into a contig. All scientific and patent publications cited in this paragraph are hereby incorporated by reference.

The patent publication WO95/35505 and U.S. Pat. Nos. 5,445,943 and 5,410,270, both hereby incorporated by reference, describe scanning multiple alleles of a plurality of loci using hybridization to arrays of oligonucleotides. These techniques are useful for each of the types of mapping discussed above.

Following the procedures described above and using a plurality of the SDFs of the present invention, any individual is genotyped. These individual genotypes are used for the identification of particular cultivars, varieties, lines, ecotypes and genetically modified plants or can serve as tools for subsequent genetic studies involving multiple phenotypic traits.

B.3 Southern Blot Hybridization

The sequences from Reference and Sequence tables or fragments thereof can be used as probes for various hybridization techniques. These techniques are useful for detecting target polynucleotides in a sample or for determining whether transgenic plants, seeds or host cells harbor a gene or sequence of interest and thus are expected to exhibit a particular trait or phenotype.

In addition, the SDFs from the invention are used to isolate additional members of gene families from the same or different species and/or orthologous genes from the same or different species. This is accomplished by hybridizing an SDF to, for example, a Southern blot containing the appropriate genomic DNA or cDNA. Given the resulting hybridization data, one of ordinary skill in the art distinguishes and isolates the correct DNA fragments by size, restriction sites, sequence and stated hybridization conditions from a gel or from a library.

Identification and isolation of orthologous genes from closely related species and alleles within a species is particularly desirable because of their potential for crop improvement. Many important crop traits, such as the solid content of tomatoes, result from the combined interactions of the products of several genes residing at different loci in the genome. Generally, alleles at each of these loci make quantitative differences to the trait. By identifying and isolating numerous alleles for each locus from within or different species, transgenic plants with various combinations of alleles are created and the effects of the combinations measured. Once a more favorable allele combination is identified, crop improvement is accomplished either through biotechnological means or by directed conventional breeding programs (Tanksley et al. Science 277:1063 (1997)). All scientific and patent publications cited in this paragraph are hereby incorporated by reference.

The results from hybridizations of the SDFs of the invention to, for example, Southern blots containing DNA from another species are also used to generate restriction fragment maps for the corresponding genomic regions. These maps provide additional information about the relative positions of restriction sites within fragments, further distinguishing mapped DNA from the remainder of the genome.

Physical maps are made by digesting genomic DNA with different combinations of restriction enzymes.

Probes for Southern blotting to distinguish individual restriction fragments can range in size from 15 to 20 nucleotides to several thousand nucleotides. More preferably, the probe is 100 to 1,000 nucleotides long for identifying members of a gene family when it is found that repetitive sequences would complicate the hybridization. For identifying an entire corresponding gene in another species, the probe is more preferably the length of the gene, typically 2,000 to 10,000 nucleotides, but probes 50-1,000 nucleotides long are also used. Some genes, however, require probes up to 1,500 nucleotides long or overlapping probes constituting the full-length sequence to span their lengths.

Also, while it is preferred that the probe be homogeneous with respect to its sequence, it is not necessary. For example, as described below, a probe representing members of a gene family having diverse sequences is generated using PCR to amplify genomic DNA or RNA templates using primers derived from SDFs that include sequences that define the gene family.

For identifying corresponding genes in another species, the next most preferable probe is a cDNA spanning the entire coding sequence, which allows all of the mRNA-coding fragment of the gene to be identified. Probes for Southern blotting are easily generated from SDFs by making primers having the sequence at the ends of the SDF and using corn or Arabidopsis genomic DNA as a template. In instances where the SDF includes sequence conserved among species, primers including the conserved sequence are used for PCR with genomic DNA from a species of interest to obtain a probe.

Similarly, if the SDF includes a domain of interest, that fragment of the SDF is used to make primers and, with appropriate template DNA, used to make a probe to identify genes containing the domain. Alternatively, the PCR products are resolved, for example by gel electrophoresis and cloned and/or sequenced. Using Southern hybridization, the variants of the domain among members of a gene family, both within and across species, are examined.

B.4.1 Isolating DNA from Related Organisms

The SDFs of the invention are used to isolate the corresponding DNA from other organisms. Either cDNA or genomic DNA is isolated. For isolating genomic DNA, a lambda, cosmid, BAC, YAC, or other large insert genomic library from the plant of interest is constructed using standard molecular biology techniques as described in detail by Sambrook et al. 1989 (Molecular Cloning: A Laboratory Manual, 2^(nd) ed. Cold Spring Harbor Laboratory Press, New York) and by Ausubel et al. 1992 (Current Protocols in Molecular Biology, Greene Publishing, New York).

To screen a phage library, for example, recombinant lambda clones are plated out on appropriate bacterial medium using an appropriate E. coli host strain. The resulting plaques are lifted from the plates using nylon or nitrocellulose filters. The plaque lifts are processed through denaturation, neutralization, and washing treatments following the standard protocols outlined by Ausubel et al. (1992). The plaque lifts are hybridized to either radioactively labeled or non-radioactively labeled SDF DNA at room temperature for about 16 hours, usually in the presence of 50% formamide and 5×SSC (sodium chloride and sodium citrate) buffer and blocking reagents. The plaque lifts are then washed at 42° C. with 1% Sodium Dodecyl Sulfate (SDS) and at a particular concentration of SSC. The SSC concentration used is dependent upon the stringency at which hybridization occurred in the initial Southern blot analysis performed. For example, if a fragment hybridized under medium stringency (e.g., Tm−20° C.), then this condition is maintained or preferably adjusted to a less stringent condition (e.g., Tm−30° C.) to wash the plaque lifts. Positive clones show detectable hybridization, e.g. by exposure to X-ray films or chromogen formation. The positive clones are then subsequently isolated for purification using the same general protocol outlined above. Once the clone is purified, restriction analysis is conducted to narrow the region corresponding to the gene of interest. The restriction analysis and succeeding subcloning steps are done using procedures described by, for example Sambrook et al. (1989) cited above.

The procedures outlined for the lambda library are essentially similar to those used for YAC library screening, except that the YAC clones are harbored in bacterial colonies. The YAC clones are plated out at reasonable density on nitrocellulose or nylon filters supported by appropriate bacterial medium in petri plates. Following the growth of the bacterial clones, the filters are processed through the denaturation, neutralization, and washing steps following the procedures of Ausubel et al. 1992. The same hybridization procedures for lambda library screening are followed.

To isolate cDNA, similar procedures using appropriately modified vectors are employed. For instance, the library is constructed in a lambda vector appropriate for cloning cDNA such as λgt11. Alternatively, the cDNA library is made in a plasmid vector. cDNA for cloning is prepared by any of the methods known in the art, but is preferably prepared as described above. Preferably, a cDNA library includes a high proportion of full-length clones.

B. 5. Isolating and/or Identifying Orthologous Genes

Probes and primers of the invention are used to identify and/or isolate polynucleotides related to those in the Reference and Sequence tables. Related polynucleotides are those that are native to other plant organisms and exhibit either similar sequence or encode polypeptides with similar biological activity. One specific example is an orthologous gene. Orthologous genes have the same functional activity. As such, orthologous genes are distinguished from homologous genes. The percentage of identity is a function of evolutionary separation and, in closely related species, the percentage of identity can be 98% to 100%. The amino acid sequence of a protein encoded by an orthologous gene can be less than 75% identical, but tends to be at least 75% or at least 80% identical, more preferably at least 90%, most preferably at least 95% identical to the amino acid sequence of the reference protein.

To find orthologous genes, the probes are hybridized to nucleic acids from a species of interest under low stringency conditions, preferably one where sequences containing as much as 40-45% mismatches are able to hybridize. This condition is established by T_(m)−40° C. to Tm−48° C. (see below). Blots are then washed under conditions of increasing stringency. It is preferable that the wash stringency be such that sequences that are 85 to 100% identical will hybridize. More preferably, sequences 90 to 100% identical hybridize and most preferably only sequences greater than 95% identical hybridize. One of ordinary skill in the art will recognize that, due to degeneracy in the genetic code, amino acid sequences that are identical can be encoded by DNA sequences as little as 67% identity or less. Thus, it is preferable, for example, to make an overlapping series of shorter probes, on the order of 24 to 45 nucleotides, and individually hybridize them to the same arrayed library to avoid the problem of degeneracy introducing large numbers of mismatches.

As evolutionary divergence increases, genome sequences also tend to diverge. Thus, one of skill will recognize that searches for orthologous genes between more divergent species require the use of lower stringency conditions compared to searches between closely related species. Also, degeneracy of the genetic code is more of a problem for searches in the genome of a species more evolutionarily distant from the species that is the source of the SDF probe sequence(s).

Therefore the method described in Bouckaert et al., U.S. Ser. No. 60/121,700 Atty. Dkt. No. 2750-117P, Client Dkt. No. 00010.001, filed Feb. 25, 1999, hereby incorporated in its entirety by reference, is applied to the SDFs of the present invention to isolate related genes from plant species which do not hybridize to the corn, Arabidopsis, soybean, rice, wheat, and other plant sequences of the Reference and Sequence tables.

The SDFs of the invention are also used as probes to search for genes that are related to the SDF within a species. Such related genes are typically considered to be members of a gene family. In such a case, the sequence similarity is often concentrated into one or a few fragments of the sequence. The fragments of similar sequence that define the gene family typically encode a fragment of a protein or RNA that has an enzymatic or structural function. The percentage of identity in the amino acid sequence of the domain that defines the gene family is preferably at least 70%, more preferably at least 80 to 95%, most preferably at least 85 to 99%. To search for members of a gene family within a species, a low stringency hybridization is usually performed, but this will depend upon the size, distribution and degree of sequence divergence of domains that define the gene family. SDFs encompassing regulatory regions are used to identify coordinately expressed genes by using the regulatory region sequence of the SDF as a probe.

In the instances where the SDFs are identified as being expressed from genes that confer a particular phenotype, then the SDFs are also used as probes to assay plants of different species for those phenotypes.

I.C. Methods to Inhibit Gene Expression

The nucleic acid molecules of the present invention are used to inhibit gene transcription and/or translation. Example of such methods include, without limitation:

Antisense Constructs;

Ribozyme Constructs;

Chimeraplast Constructs;

Co-Suppression;

Transcriptional Silencing; and

Other Methods of Gene Expression.

C.1 Antisense

In some instances it is desirable to suppress expression of an endogenous or exogenous gene. A well-known instance is the FLAVOR-SAVOR™ tomato, in which the gene encoding ACC synthase is inactivated by an antisense approach, thus delaying softening of the fruit after ripening. See for example, U.S. Pat. No. 5,859,330; U.S. Pat. No. 5,723,766; Oeller, et al, Science, 254:437-439 (1991); and Hamilton et al, Nature, 346:284-287 (1990). As another example, timing of flowering is controlled by suppression of the FLOWERING LOCUS C (FLC). High levels of this transcript are associated with late flowering, while absence of FLC is associated with early flowering (S. D. Michaels et al., Plant Cell 11:949 (1999). Other examples include the transition of apical meristem from leaf and shoot production to flowering which is regulated by TERMINAL FLOWER1, APETALA1 and LEAFY. Suppressing TFL1 expression induce a transition from shoot production to flowering (S. J. Liljegren, Plant Cell 11:1007 (1999)). In yet another example, arrested ovule development and female sterility result from suppression of the ethylene forming enzyme, but can be reversed by application of ethylene (D. De Martinis et al., Plant Cell 11:1061 (1999)). The ability to manipulate female fertility of plants is useful in increasing fruit production and creating hybrids.

Some polynucleotide SDFs in the Reference and Sequence tables represent sequences that are expressed in corn, wheat, rice, soybean Arabidopsis and/or other plants. Thus the invention includes using these sequences to generate antisense constructs to inhibit translation and/or degradation of transcripts of said SDFs, typically in a plant cell.

To accomplish this, a polynucleotide segment from the desired gene that hybridizes to the mRNA expressed from the desired gene (the “antisense segment”) is operably linked to a promoter such that the antisense strand of RNA is transcribed when the construct is present in a host cell. A regulated promoter is used in the construct to control transcription of the antisense segment so that transcription occurs only under desired circumstances.

The antisense segment introduced is typically substantially identical to at least a fragment of the endogenous gene or genes to be repressed. The sequence, however, need not be perfectly identical to inhibit expression. Further, the antisense product may hybridize to the untranslated region instead of or in addition to the coding sequence of the gene. The vectors of the present invention designed such that the inhibitory effect applies to other proteins within a family of genes exhibiting homology or substantial homology to the target gene.

For antisense suppression, the introduced antisense segment sequence also need not be full length relative to either the primary transcription product or the fully processed mRNA. Generally, a higher percentage of sequence identity is used to compensate for the use of a shorter sequence. Furthermore, the introduced sequence need not have the same intron or exon pattern, and homology of non-coding segments are equally effective. Normally, a sequence of between about 30 or 40 nucleotides and the full length of the transcript can be used, although a sequence of at least about 100 nucleotides is preferred, a sequence of at least about 200 nucleotides is more preferred, and a sequence of at least about 500 nucleotides is especially preferred.

C.2. Ribozymes

It is also contemplated that gene constructs representing ribozymes and based on the SDFs in the Reference and Sequence tables tables and fragment thereof are an object of the invention. Ribozymes are also used to inhibit expression of genes by suppressing the translation of the mRNA into a polypeptide. It is possible to design ribozymes that specifically pair with virtually any target RNA and cleave the phosphodiester backbone at a specific location, thereby functionally inactivating the target RNA. In carrying out this cleavage, the ribozyme is not itself altered, and is thus capable of recycling and cleaving other molecules, making it a true enzyme. The inclusion of ribozyme sequences within antisense RNAs confers RNA-cleaving activity upon them, thereby increasing the activity of the constructs.

A number of classes of ribozymes are known. One class of ribozymes is derived from a number of small circular RNAs, which are capable of self-cleavage and replication in plants. The RNAs replicate either alone (viroid RNAs) or with a helper virus (satellite RNAs). Examples include RNAs from avocado sunblotch viroid and the satellite RNAs from tobacco ringspot virus, lucerne transient streak virus, velvet tobacco mottle virus, solanum nodiflorum mottle virus and subterranean clover mottle virus. The design and use of target RNA-specific ribozymes is described in Haseloff et al. Nature, 334:585 (1988).

Like the antisense constructs above, the ribozyme sequence fragment necessary for pairing need not be identical to the target nucleotides to be cleaved, nor identical to the sequences in the Reference and Sequence tables or fragments thereof. Ribozymes are constructed by combining the ribozyme sequence and some fragment of the target gene which allows recognition of the target gene mRNA by the resulting ribozyme molecule. Generally, the sequence in the ribozyme capable of binding to the target sequence exhibits a percentage of sequence identity with at least 80%, preferably with at least 85%, more preferably with at least 90% and most preferably with at least 95%, even more preferably, with at least 96%, 97%, 98% or 99% sequence identity to some fragment of a sequence in the Reference and Sequence tables or the complements thereof. The ribozyme is equally effective in inhibiting mRNA translation by cleaving either in the untranslated or coding regions. Generally, a higher percentage of sequence identity is used to compensate for the use of a shorter sequence. Furthermore, the introduced sequence need not have the same intron or exon pattern, and homology of non-coding segments are equally effective.

C.3. Chimeraplasts

The SDFs of the invention, such as those described by Reference and Sequence tables are also used to construct chimeraplasts that introduced into a cell to produce at least one specific nucleotide change in a sequence corresponding to the SDF of the invention. A chimeraplast is an oligonucleotide comprising DNA and/or RNA that specifically hybridizes to a target region in a manner which creates a mismatched base-pair. This mismatched base-pair signals the cell's repair enzyme machinery which acts on the mismatched region and results in the replacement, insertion or deletion of designated nucleotide(s). The altered sequence is then expressed by the cell's normal cellular mechanisms. Chimeraplasts are designed to repair mutant genes, modify genes, introduce site-specific mutations, and/or act to interrupt or alter normal gene function (U.S. Pat. Nos. 6,010,907 and 6,004,804; and PCT Pub. No. WO99/58723 and WO99/07865).

C.4. Sense Suppression

The SDFs of the Reference and Sequence tables of the present invention are also useful to modulate gene expression by sense suppression. Sense suppression represents another method of gene suppression that introduces at least one exogenous copy or fragment of the endogenous sequence to be suppressed.

Introduction of expression cassettes in which a nucleic acid is configured in the sense orientation with respect to the promoter into the chromosome of a plant or by a self-replicating virus is an effective means by which to induce degradation of mRNAs of target genes. For an example of the use of this method to modulate expression of endogenous genes see, Napoli et al., The Plant Cell 2:279 (1990), and U.S. Pat. Nos. 5,034,323, 5,231,020, and 5,283,184. Inhibition of expression requires some transcription of the introduced sequence.

For sense suppression, the introduced sequence generally is substantially identical to the endogenous sequence intended to be inactivated. The minimal percentage of sequence identity is typically greater than about 65%, but a higher percentage of sequence identity might exert a more effective reduction in the level of normal gene products. Sequence identity of more than about 80% is preferred, though about 95% to absolute identity is most preferred. As with antisense regulation, the effect applies to any other proteins within a similar family of genes exhibiting homology or substantial homology to the suppressing sequence.

C.5. Other Methods to Inhibit Gene Expression

Yet another means of suppressing gene expression is to insert a polynucleotide into the gene of interest to disrupt transcription or translation of the gene.

Low frequency homologous recombination is used to target a polynucleotide insert to a gene by flanking the polynucleotide insert with sequences that are substantially similar to the gene to be disrupted. Sequences from the Reference and Sequence tables, fragments thereof and substantially similar sequences thereto are used for homologous recombination.

In addition, random insertion of polynucleotides into a host cell genome is used to disrupt the gene of interest (Azpiroz-Leehan et al., Trends in Genetics 13:152 (1997). In this method, screening for clones from a library containing random insertions is preferred to identifying those that have polynucleotides inserted into the gene of interest. Such screening is performed using probes and/or primers described above based on sequences from Reference and Sequence tables, fragments thereof, and substantially similar sequence thereto. The screening is also performed by selecting clones or R₁ plants having a desired phenotype.

I.D. Methods of Functional Analysis

The constructs described in the methods under I.C. above are used to determine the function of the polypeptide encoded by the gene that is targeted by the constructs.

Down-regulating the transcription and translation of the targeted gene in the host cell or organisms, such as a plant, produces phenotypic changes as compared to a wild-type cell or organism. In addition, in vitro assays are used to determine if any biological activity, such as calcium flux, DNA transcription, nucleotide incorporation, etc., are being modulated by the down-regulation of the targeted gene.

Coordinated regulation of sets of genes, e.g. those contributing to a desired polygenic trait, is sometimes necessary to obtain a desired phenotype. SDFs of the invention representing transcription activation and DNA binding domains are assembled into hybrid transcriptional activators. These hybrid transcriptional activators are used with their corresponding DNA elements (i.e. those bound by the DNA-binding SDFs) to effect coordinated expression of desired genes (J. J. Schwarz et al., Mol. Cell. Biol. 12:266 (1992), A. Martinez et al., Mol. Gen. Genet. 261:546 (1999)).

The SDFs of the invention are also used in the two-hybrid genetic systems to identify networks of protein-protein interactions (L. McAlister-Henn et al., Methods 19:330 (1999), J. C. Hu et al., Methods 20:80 (2000), M. Golovkin et al., J. Biol. Chem. 274:36428 (1999), K. Ichimura et al., Biochem. Biophys. Res. Comm. 253:532 (1998)). The SDFs of the invention also are used in various expression display methods to identify important protein-DNA interactions (e.g. B. Luo et al., J. Mol. Biol. 266:479 (1997)).

I.E. UTRs and Junctions

Polynucleotides comprising untranslated (UTR) sequences and intron/exon junctions are also within the scope of the invention. UTR sequences include introns and 5′ or 3′ untranslated regions (5′ UTRs or 3′ UTRs). Fragments of the sequences shown in the Reference and Sequence tables comprise UTRs and intron/exon junctions.

Some of these fragments of SDFs, especially UTRs, have regulatory functions related to, for example, translation rate and mRNA stability. Thus, these fragments of SDFs are isolated for use as elements of gene constructs for regulated production of polynucleotides encoding desired polypeptides.

Some introns of genomic DNA segments also have regulatory functions. Sometimes regulatory elements, especially transcription enhancer or suppressor elements, are found within introns. Also, elements related to stability of heteronuclear RNA and efficiency of splicing and of transport to the cytoplasm for translation are found in intron elements. Thus, these segments also find use as elements of expression vectors intended for use to transform plants.

Just as with promoters UTR sequences and intron/exon junctions vary from those shown in the Reference and Sequence tables. Such changes from those sequences preferably do not affect the regulatory activity of the UTRs or intron/exon junction sequences on expression, transcription, or translation unless selected to do so. However, in some instances, down- or up-regulation of such activity may be desired to modulate traits or phenotypic or in vitro activity.

I.F Coding Sequences

Isolated polynucleotides of the invention include coding sequences that encode polypeptides comprising an amino acid sequence encoded by sequences described in the Reference and Sequence tables.

A nucleotide sequence encodes a polypeptide if a cell (or a cell free in vitro system) expressing that nucleotide sequence produces a polypeptide having the recited amino acid sequence when the nucleotide sequence is transcribed and the primary transcript is subsequently processed and translated by a host cell (or a cell free in vitro system) harboring the nucleic acid. Thus, an isolated nucleic acid that encodes a particular amino acid sequence is a genomic sequence comprising exons and introns or a cDNA sequence that represents the product of splicing thereof. An isolated nucleic acid encoding an amino acid sequence also encompasses heteronuclear RNA, which contains sequences that are spliced out during expression, and mRNA, which lacks those sequences.

Coding sequences are constructed using chemical synthesis techniques or by isolating coding sequences or by modifying such synthesized or isolated coding sequences as described above.

In addition to coding sequences encoding the polypeptide sequences of the Reference and Sequence tables, which are native to corn, Arabidopsis, soybean, rice, wheat, and other plants, the isolated polynucleotides are polynucleotides that encode variants, fragments, and fusions of those native proteins. Such polypeptides are described below in part II.

In variant polynucleotides generally, the number of substitutions, deletions or insertions is preferably less than 20%, more preferably less than 15%; even more preferably less than 10%, 5%, 3% or 1% of the number of nucleotides comprising a particularly exemplified sequence. It is generally expected that non-degenerate nucleotide sequence changes that result in 1 to 10, more preferably 1 to 5 and most preferably 1 to 3 amino acid insertions, deletions or substitutions do not greatly affect the function of an encoded polypeptide. The most preferred embodiments are those wherein 1 to 20, preferably 1 to 10, most preferably 1 to 5 nucleotides are added to, or deleted from and/or substituted in the sequences specifically disclosed in the Reference and Sequence tables or fragments thereof.

Insertions or deletions in polynucleotides intended to be used for encoding a polypeptide preferably preserve the reading frame. This consideration is not so important in instances when the polynucleotide is intended to be used as a hybridization probe.

II. Polypeptides and Proteins

IIA. Native polypeptides and proteins

Polypeptides within the scope of the invention include both native proteins as well as variants, fragments, and fusions thereof. Polypeptides of the invention are those encoded by any of the six reading frames of sequences shown in the Reference and Sequence tables, preferably encoded by the three frames reading in the 5′ to 3′ direction of the sequences as shown.

Native polypeptides include the proteins encoded by the sequences shown in the Reference and Sequence tables. Such native polypeptides include those encoded by allelic variants.

Polypeptide and protein variants will exhibit at least 75% sequence identity to those native polypeptides of the Reference and Sequence tables. More preferably, the polypeptide variants will exhibit at least 85% sequence identity; even more preferably, at least 90% sequence identity; more preferably at least 95%, 96%, 97%, 98%, or 99% sequence identity. Fragments of polypeptide or fragments of polypeptides exhibit similar percentages of sequence identity to the relevant fragments of the native polypeptide. Fusions exhibit a similar percentage of sequence identity in that fragment of the fusion represented by the variant of the native peptide.

Furthermore, polypeptide variants exhibit at least one of the functional properties of the native protein. Such properties include, without limitation, protein interaction, DNA interaction, biological activity, immunological activity, receptor binding, signal transduction, transcription activity, growth factor activity, secondary structure, three-dimensional structure, etc. As to properties related to in vitro or in vivo activities, the variants preferably exhibit at least 60% of the activity of the native protein; more preferably at least 70%, even more preferably at least 80%, 85%, 90% or 95% of at least one activity of the native protein.

One type of variant of native polypeptides comprises amino acid substitutions, deletions and/or insertions. Conservative substitutions are preferred to maintain the function or activity of the polypeptide.

Within the scope of percentage of sequence identity described above, a polypeptide of the invention may have additional individual amino acids or amino acid sequences inserted into the polypeptide in the middle thereof and/or at the N-terminal and/or C-terminal ends thereof. Likewise, some of the amino acids or amino acid sequences may be deleted from the polypeptide.

A.1 Antibodies

Isolated polypeptides are utilized to produce antibodies. Polypeptides of the invention are generally used, for example, as antigens for raising antibodies by known techniques. The resulting antibodies are useful as reagents for determining the distribution of the antigen protein within the tissues of a plant or within a cell of a plant. The antibodies are also useful for examining the production level of proteins in various tissues, for example in a wild-type plant or following genetic manipulation of a plant, by methods such as Western blotting.

Antibodies of the present invention, both polyclonal and monoclonal, are prepared by conventional methods. In general, the polypeptides of the invention are first used to immunize a suitable animal, such as a mouse, rat, rabbit, or goat. Rabbits and goats are preferred for the preparation of polyclonal sera due to the volume of serum obtainable and the availability of labeled anti-rabbit and anti-goat antibodies as detection reagents. Immunization is generally performed by mixing or emulsifying the protein in saline, preferably in an adjuvant such as Freund's complete adjuvant, and injecting the mixture or emulsion parenterally (generally subcutaneously or intramuscularly). A dose of 50-200 μg/injection is typically sufficient. Immunization is generally boosted 2-6 weeks later with one or more injections of the protein in saline, preferably using Freund's incomplete adjuvant. One may alternatively generate antibodies by in vitro immunization using methods known in the art, which for the purposes of this invention is considered equivalent to in vivo immunization.

Polyclonal antisera is obtained by bleeding the immunized animal into a glass or plastic container, incubating the blood at 25° C. for one hour, followed by incubating the blood at 4° C. for 2-18 hours. The serum is recovered by centrifugation (e.g., 1,000×g for 10 minutes). About 20-50 ml per bleed may be obtained from rabbits.

Monoclonal antibodies are prepared using the method of Kohler and Milstein, Nature 256: 495 (1975), or modification thereof. Typically, a mouse or rat is immunized as described above. However, rather than bleeding the animal to extract serum, the spleen (and optionally several large lymph nodes) is removed and dissociated into single cells. If desired, the spleen cells can be screened (after removal of nonspecifically adherent cells) by applying a cell suspension to a plate or well coated with the protein antigen. B-cells producing membrane-bound immunoglobulin specific for the antigen bind to the plate and are not rinsed away with the rest of the suspension. Resulting B-cells, or all dissociated spleen cells, are then induced to fuse with myeloma cells to form hybridomas and are cultured in a selective medium (e.g., hypoxanthine, aminopterin, thymidine medium, “HAT”). The resulting hybridomas are plated by limiting dilution, and are assayed for the production of antibodies which bind specifically to the immunizing antigen (and which do not bind to unrelated antigens). The selected Mab-secreting hybridomas are then cultured either in vitro (e.g., in tissue culture bottles or hollow fiber reactors) or in vivo (as ascites in mice).

Other methods for sustaining antibody-producing B-cell clones, such as by EBV transformation, are known.

If desired, the antibodies (whether polyclonal or monoclonal) may be labeled using conventional techniques. Suitable labels include fluorophores, chromophores, radioactive atoms (particularly ³²P and ¹²⁵I), electron-dense reagents, enzymes and ligands having specific binding partners. Enzymes are typically detected by their activity. For example, horseradish peroxidase is usually detected by its ability to convert 3,3′,5,5′-tetramethylbenzidine (TNB) to a blue pigment, quantifiable with a spectrophotometer.

A.2 In Vitro Applications of Polypeptides

Some polypeptides of the invention will have enzymatic activities that are useful in vitro. For example, the soybean trypsin inhibitor (Kunitz) family is one of the numerous families of proteinase inhibitors. It comprises plant proteins which have inhibitory activity against serine proteinases from the trypsin and subtilisin families, thiol proteinases and aspartic proteinases. Thus, these peptides find in vitro use in protein purification protocols and in therapeutic settings requiring topical application of protease inhibitors.

Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) (ALAD) catalyzes the second step in the biosynthesis of heme, the condensation of two molecules of 5-aminolevulinate to form porphobilinogen and is also involved in chlorophyll biosynthesis (Kaczor et al. (1994) Plant Physiol. 1-4: 1411-7; Smith (1988) Biochem. J. 249: 423-8; Schneider (1976) Z. naturforsch. [C] 31: 55-63). Thus, ALAD proteins can be used as catalysts in synthesis of heme derivatives. Enzymes of biosynthetic pathways generally can be used as catalysts for in vitro synthesis of the compounds representing products of the pathway.

Polypeptides encoded by SDFs of the invention are engineered to provide purification reagents to identify and purify additional polypeptides that bind to them. This allows one to identify proteins that function as multimers or elucidate signal transduction or metabolic pathways. In the case of DNA binding proteins, the polypeptide are used in a similar manner to identify the DNA determinants of specific binding (S. Pierrou et al., Anal. Biochem. 229:99 (1995), S. Chusacultanachai et al., J. Biol. Chem. 274:23591 (1999), Q. Lin et al., J. Biol. Chem. 272:27274 (1997)).

II.B. Polypeptide Variants, Fragments, and Fusions

Generally, variants, fragments, or fusions of the polypeptides encoded by the maximum length sequence (MLS) can exhibit at least one of the activities of the identified domains and/or related polypeptides described in Sections (C) and (D) of The Reference tables corresponding to the MLS of interest.

II.B1 Variants

A type of variant of the native polypeptides comprises amino acid substitutions. Conservative substitutions, described above (see II.), are preferred to maintain the function or activity of the polypeptide. Such substitutions include conservation of charge, polarity, hydrophobicity, size, etc. For example, one or more amino acid residues within the sequence is substituted with another amino acid of similar polarity that acts as a functional equivalent, for example providing a hydrogen bond in an enzymatic catalysis. Substitutes for an amino acid within an exemplified sequence are preferably made among the members of the class to which the amino acid belongs. For example, the nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid.

Within the scope of percentage of sequence identity described above, a polypeptide of the invention may have additional individual amino acids or amino acid sequences inserted into the polypeptide in the middle thereof and/or at the N-terminal and/or C-terminal ends thereof. Likewise, some of the amino acids or amino acid sequences may be deleted from the polypeptide. Amino acid substitutions may also be made in the sequences; conservative substitutions being preferred.

One preferred class of variants are those that comprise (1) the domain of an encoded polypeptide and/or (2) residues conserved between the encoded polypeptide and related polypeptides. For this class of variants, the encoded polypeptide sequence is changed by insertion, deletion, or substitution at positions flanking the domain and/or conserved residues.

Another class of variants includes those that comprise an encoded polypeptide sequence that is changed in the domain or conserved residues by a conservative substitution.

Yet another class of variants includes those that lack one of the in vitro activities, or structural features of the encoded polypeptides. One example is polypeptides or proteins produced from genes comprising dominant negative mutations. Such a variant may comprise an encoded polypeptide sequence with non-conservative changes in a particular domain or group of conserved residues.

II.A.2 Fragments

Fragments of particular interest are those that comprise a domain identified for a polypeptide encoded by an MLS of the instant invention and variants thereof. Also, fragments that comprise at least one region of residues conserved between an MLS encoded polypeptide and its related polypeptides are of great interest. Fragments are sometimes useful as polypeptides corresponding to genes comprising dominant negative mutations.

II.A.3 Fusions

Of interest are chimeras comprising (1) a fragment of the MLS encoded polypeptide or variants thereof of interest and (2) a fragment of a polypeptide comprising the same domain. For example, an AP2 helix encoded by a MLS of the invention fused to second AP2 helix from ANT protein, which comprises two AP2 helices. The present invention also encompasses fusions of MLS encoded polypeptides, variants, or fragments thereof fused with related proteins or fragments thereof.

Definition of Domains

The polypeptides of the invention possess identifying domains as shown in The Reference tables, which indicate specific domains within the MLS encoded polypeptides. In addition, the domains within the MLS encoded polypeptide are defined by the region that exhibits at least 70% sequence identity with the consensus sequences listed in the detailed description below of each of the domains.

The majority of the protein domain descriptions given in the protein domain table are obtained from the Prosite and the Pfam websites available on the internet.

A. Activities of Polypeptides Comprising Signal Peptides

Polypeptides comprising signal peptides are a family of proteins that are typically targeted to (1) a particular organelle or intracellular compartment, (2) interact with a particular molecule or (3) for secretion outside of a host cell. Example of polypeptides comprising signal peptides include, without limitation, secreted proteins, soluble proteins, receptors, proteins retained in the ER, etc.

These proteins comprising signal peptides are useful to modulate ligand-receptor interactions, cell-to-cell communication, signal transduction, intracellular communication, and activities and/or chemical cascades that take part in an organism outside or within of any particular cell.

One class of such proteins are soluble proteins which are transported out of the cell. These proteins act as ligands that bind to receptor to trigger signal transduction or to permit communication between cells.

Another class is receptor proteins which also comprise a retention domain that lodges the receptor protein in the membrane when the cell transports the receptor to the surface of the cell. Like the soluble ligands, receptors also modulate signal transduction and communication between cells.

In addition the signal peptide itself can serve as a ligand for some receptors. An example is the interaction of the ER targeting signal peptide with the signal recognition particle (SRP). Here, the SRP binds to the signal peptide, halting translation, and the resulting SRP complex then binds to docking proteins located on the surface of the ER, prompting transfer of the protein into the ER.

A description of signal peptide residue composition is described below in Subsection IV.C.1.

III. Methods of Modulating Polypeptide Production

It is contemplated that polynucleotides of the invention are incorporated into a host cell or in-vitro system to modulate polypeptide production. For instance, the SDFs prepared as described herein are used to prepare expression cassettes useful in a number of techniques for suppressing or enhancing expression.

An example are polynucleotides comprising sequences to be transcribed, such as coding sequences, of the present invention are inserted into nucleic acid constructs to modulate polypeptide production. Typically, such sequences to be transcribed are heterologous to at least one element of the nucleic acid construct to generate a chimeric gene or construct.

Another example of useful polynucleotides are nucleic acid molecules comprising regulatory sequences of the present invention. Chimeric genes or constructs are generated when the regulatory sequences of the invention linked to heterologous sequences in a vector construct. Within the scope of the invention are such chimeric gene and/or constructs.

Also within the scope of the invention are nucleic acid molecules, whereof at least a part or fragment of these DNA molecules are presented in the Reference and Sequence tables of the present application, and wherein the coding sequence is under the control of its own promoter and/or its own regulatory elements. Such molecules are useful for transforming the genome of a host cell or an organism regenerated from said host cell for modulating polypeptide production.

Additionally, a vector capable of producing the oligonucleotide can be inserted into the host cell to deliver the oligonucleotide.

More detailed description of components to be included in vector constructs are described both above and below.

Whether the chimeric vectors or native nucleic acids are utilized, such polynucleotides are incorporated into a host cell to modulate polypeptide production. Native genes and/or nucleic acid molecules are effective when exogenous to the host cell.

Methods of modulating polypeptide expression includes, without limitation:

Suppression methods, such as

-   -   Antisense     -   Ribozymes     -   Co-suppression     -   Insertion of Sequences into the Gene to be Modulated     -   Regulatory Sequence Modulation.

as well as Methods for Enhancing Production, such as

-   -   Insertion of Exogenous Sequences; and     -   Regulatory Sequence Modulation.

III.A. Suppression

Expression cassettes of the invention are used to suppress expression of endogenous genes which comprise the SDF sequence. Inhibiting expression is useful, for instance, to tailor the ripening characteristics of a fruit (Oeller et al., Science 254:437 (1991)) or to influence seed size (WO98/07842) or to provoke cell ablation (Mariani et al., Nature 357: 384-387 (1992).

As described above, a number of methods are used to inhibit gene expression in plants, such as antisense, ribozyme, introduction of exogenous genes into a host cell, insertion of a polynucleotide sequence into the coding sequence and/or the promoter of the endogenous gene of interest and the like.

III.A.1. Antisense

An expression cassette as described above transformed into host cell or plant to produce an antisense strand of RNA. For plant cells, antisense RNA inhibits gene expression by preventing the accumulation of mRNA which encodes the enzyme of interest, see, e.g., Sheehy et al., Proc. Nat. Acad. Sci. USA, 85:8805 (1988), and Hiatt et al., U.S. Pat. No. 4,801,340.

III.A.2. Ribozymes

Similarly, ribozyme constructs are transformed into a plant to cleave mRNA and down-regulate translation.

III.A.3. Co-Suppression

Another method of suppression occurs by introducing an exogenous copy of the gene to be suppressed. Introduction of expression cassettes in which a nucleic acid is configured in the sense orientation with respect to the promoter prevents the accumulation of mRNA. A detailed description of this method is described above.

III.A.4. Insertion of Sequences into the Gene to be Modulated

Yet another means of suppressing gene expression is to insert a polynucleotide into the gene of interest to disrupt transcription or translation of the gene.

Homologous recombination could be used to target a polynucleotide insert to a gene using the Cre-Lox system (A. C. Vergunst et al., Nucleic Acids Res. 26:2729 (1998), A. C. Vergunst et al., Plant Mol. Biol. 38:393 (1998), H. Albert et al., Plant J. 7:649 (1995)).

In addition, random insertion of polynucleotides into a host cell genome are also used to disrupt the gene of interest (Azpiroz-Leehan et al., Trends in Genetics 13:152 (1997)). In this method, screening for clones from a library containing random insertions is preferred for identifying those that have polynucleotides inserted into the gene of interest. Such screening is performed using probes and/or primers described above based on sequences from the Reference and Sequence tables, fragments thereof, and substantially similar sequence thereto. The screening is also performed by selecting clones or any transgenic plants having a desired phenotype.

III.A.5. Regulatory Sequence Modulation

The SDFs described in the Reference and Sequence tables or polynucleotides encoding polypeptides of the Protein Group or Protein Group Matrix tables, and fragments thereof are examples of nucleotides of the invention that contain regulatory sequences that can be used to suppress or inactivate transcription and/or translation from a gene of interest as discussed in I.C.5.

III.A.6. Genes Comprising Dominant-Negative Mutations

When suppression of production of the endogenous, native protein is desired it is often helpful to express a gene comprising a dominant negative mutation. Genes comprising dominant negative mutations produce a variant polypeptide that is capable of competing with the native polypeptide, but which does not produce the native result. Consequently, over-expression of genes comprising these mutations titrate out an undesired activity of the native protein. For example, the product from a gene comprising a dominant negative mutation of a receptor is used to constitutively activate or suppress a signal transduction cascade, allowing examination of the phenotype and thus the trait(s) controlled by that receptor and pathway. Alternatively, the protein arising from the gene comprising a dominant-negative mutation is an inactive enzyme still capable of binding to the same substrate as the native protein and therefore competes with such native proteins.

Products from genes comprising dominant-negative mutations also act upon the native protein itself to prevent activity. For example, the native protein may be active only as a homo-multimer or as one subunit of a hetero-multimer. Incorporation of an inactive subunit into the multimer with native subunit(s) inhibits activity.

Thus, gene function is modulated in host cells of interest by insertion into these cells vector constructs comprising a gene comprising a dominant-negative mutation.

III.B. Enhanced Expression

Enhanced expression of a gene of interest in a host cell is accomplished by either (1) insertion of an exogenous gene; or (2) promoter modulation.

III.B.1. Insertion of an Exogenous Gene

Insertion of an expression construct encoding an exogenous gene boosts the number of gene copies expressed in a host cell.

Such expression constructs comprise genes that either encode the native protein that is of interest or that encode a variant that exhibits enhanced activity as compared to the native protein. Such genes encoding proteins of interest are constructed from the sequences from the Reference and Sequence tables, fragments thereof, and substantially similar sequence thereto.

Such an exogenous gene includes a constitutive promoter permitting expression in any cell in a host organism or a promoter that directs transcription only in particular cells or times during a host cell life cycle or in response to environmental stimuli.

III.B.2. Regulatory Sequence Modulation

The SDFs of the Reference and Sequence tables, and fragments thereof, contain regulatory sequences that are used to enhance expression of a gene of interest. For example, some of these sequences contain useful enhancer elements. In some cases, duplication of enhancer elements or insertion of exogenous enhancer elements increases expression of a desired gene from a particular promoter. As other examples, all Il promoters require binding of a regulatory protein to be activated, while some promoters may need a protein that signals a promoter binding protein to expose a polymerase binding site. In either case, over-production of such proteins are used to enhance expression of a gene of interest by increasing the activation time of the promoter.

Such regulatory proteins are encoded by some of the sequences in the Reference and Sequence tables, fragments thereof, and substantially similar sequences thereto.

Coding sequences for these proteins are constructed as described above.

IV. Gene Constructs and Vector Construction

To use isolated SDFs of the present invention or a combination of them or parts and/or mutants and/or fusions of said SDFs in the above techniques, recombinant DNA vectors that comprise said SDFs and are suitable for transformation of cells, such as plant cells, are usually prepared. The SDF construct are made using standard recombinant DNA techniques (Sambrook et al. 1989) and is introduced to the species of interest by Agrobacterium mediated transformation or by other means of transformation (e.g. particle gun bombardment) as referenced below.

The vector backbone can be any of those typical in the art such as plasmids, viruses, artificial chromosomes, BACs, YACs, PACs and vectors of the sort described by

(a) BAC: Shizuya et al., Proc. Natl. Acad. Sci. USA 89: 8794-8797 (1992); Hamilton et al., Proc. Natl. Acad. Sci. USA 93: 9975-9979 (1996);

(b) YAC: Burke et al., Science 236:806-812 (1987);.

(c) PAC: Sternberg N. et al., Proc Natl Acad Sci USA. Jan; 87(1):103-7 (1990);

(d) Bacteria-Yeast Shuttle Vectors: Bradshaw et al., Nucl Acids Res 23: 4850-4856 (1995);

(e) Lambda Phage Vectors: Replacement Vector, e.g., Frischauf et al., J. Mol. Biol 170: 827-842 (1983); or Insertion vector, e.g., Huynh et al., In: Glover N M (ed) DNA Cloning: A practical Approach, Vol. 1 Oxford: IRL Press (1985);

(f) T-DNA gene fusion vectors: Walden et al., Mol Cell Biol 1: 175-194 (1990); and

(g) Plasmid vectors: Sambrook et al., infra.

Typically, a vector comprises the exogenous gene, which in its turn comprises an SDF of the present invention to be introduced into the genome of a host cell, and which gene may be an antisense construct, a ribozyme construct chimeraplast, or a coding sequence with any desired transcriptional and/or translational regulatory sequences, such as promoters, UTRs, and 3′ end termination sequences. Vectors of the invention also include origins of replication, scaffold attachment regions (SARs), markers, homologous sequences, introns, etc.

A DNA sequence coding for the desired polypeptide, for example a cDNA sequence encoding a full length protein, are preferably combined with transcriptional and translational initiation regulatory sequences which direct the transcription of the sequence from the gene in the intended tissues of the transformed plant. For example, for over-expression, a plant promoter fragment is employed that direct transcription of the gene in all tissues of a regenerated plant. Alternatively, the plant promoter directs transcription of an SDF of the invention in a specific tissue (tissue-specific promoters) or is otherwise under more precise environmental control (inducible promoters).

If proper polypeptide production is desired, a polyadenylation region at the 3′-end of the coding region is typically included. The polyadenylation region is derived from the natural gene, from a variety of other plant genes, or from T-DNA.

The vector comprising the sequences from genes or SDF or the invention comprises a marker gene that confers a selectable phenotype on plant cells. The vector includes promoter and coding sequence, for instance. For example, the marker may encode biocide resistance, particularly antibiotic resistance, such as resistance to kanamycin, G418, bleomycin, hygromycin, or herbicide resistance, (e.g. resistance to chlorosulfuron or phosphinotricin).

IV.A. Coding Sequences

Generally, the sequence in the transformation vector and to be introduced into the genome of the host cell does not need to be absolutely identical to an SDF of the present invention. Also, it is not necessary for it to be full length, relative to either the primary transcription product or fully processed mRNA. Furthermore, the introduced sequence need not have the same intron or exon pattern as a native gene. Also, heterologous non-coding segments can be incorporated into the coding sequence without changing the desired amino acid sequence of the polypeptide to be produced.

IV.B. Promoters

As explained above, introducing an exogenous SDF from the same species or an orthologous SDF from another species is useful to modulate the expression of a native gene corresponding to that SDF of interest. Such an SDF construct is under the control of either a constitutive promoter or a highly regulated inducible promoter (e.g., a copper inducible promoter). The promoter of interest is initially either endogenous or heterologous to the species in question. When re-introduced into the genome of said species, such promoter becomes exogenous to said species. Over-expression of an SDF transgene leads to co-suppression of the homologous endogeneous sequence thereby creating some alterations in the phenotypes of the transformed species as demonstrated by similar analysis of the chalcone synthase gene (Napoli et al., Plant Cell 2:279 (1990) and van der Krol et al., Plant Cell 2:291 (1990)). If an SDF is found to encode a protein with desirable characteristics, its over-production is controlled so that its accumulation is manipulated in an organ- or tissue-specific manner utilizing a promoter having such specificity.

Likewise, if the promoter of an SDF (or an SDF that includes a promoter) is found to be tissue-specific or developmentally regulated, such a promoter is utilized to drive or facilitate the transcription of a specific gene of interest (e.g., seed storage protein or root-specific protein). Thus, the level of accumulation of a particular protein is manipulated or its spatial localization in an organ- or tissue-specific manner is altered.

IV.C Signal Peptides

SDFs of the present invention containing signal peptides are indicated in the Reference and Sequence tables. In some cases it may be desirable for the protein encoded by an introduced exogenous or orthologous SDF to be targeted (1) to a particular organelle intracellular compartment, (2) to interact with a particular molecule such as a membrane molecule or (3) for secretion outside of the cell harboring the introduced SDF. This is accomplished using a signal peptide.

Signal peptides direct protein targeting, are involved in ligand-receptor interactions and act in cell to cell communication. Many proteins, especially soluble proteins, contain a signal peptide that targets the protein to one of several different intracellular compartments. In plants, these compartments include, but are not limited to, the endoplasmic reticulum (ER), mitochondria, plastids (such as chloroplasts), the vacuole, the Golgi apparatus, protein storage vessicles (PSV) and, in general, membranes. Some signal peptide sequences are conserved, such as the Asn-Pro-Ile-Arg amino acid motif found in the N-terminal propeptide signal that targets proteins to the vacuole (Marty (1999) The Plant Cell 11: 587-599). Other signal peptides do not have a consensus sequence per se, but are largely composed of hydrophobic amino acids, such as those signal peptides targeting proteins to the ER (Vitale and Denecke (1999) The Plant Cell 11: 615-628). Still others do not appear to contain either a consensus sequence or an identified common secondary sequence, for instance the chloroplast stromal targeting signal peptides (Keegstra and Cline (1999) The Plant Cell 11: 557-570). Furthermore, some targeting peptides are bipartite, directing proteins first to an organelle and then to a membrane within the organelle (e.g. within the thylakoid lumen of the chloroplast; see Keegstra and Cline (1999) The Plant Cell 11: 557-570). In addition to the diversity in sequence and secondary structure, placement of the signal peptide is also varied. Proteins destined for the vacuole, for example, have targeting signal peptides found at the N-terminus, at the C-terminus and at a surface location in mature, folded proteins. Signal peptides also serve as ligands for some receptors.

These characteristics of signal proteins are used to more tightly control the phenotypic expression of introduced SDFs. In particular, associating the appropriate signal sequence with a specific SDF allows sequestering of the protein in specific organelles (plastids, as an example), secretion outside of the cell, targeting interaction with particular receptors, etc. Hence, the inclusion of signal proteins in constructs involving the SDFs of the invention increases the range of manipulation of SDF phenotypic expression. The nucleotide sequence of the signal peptide is isolated from characterized genes using common molecular biological techniques or is synthesized in vitro.

In addition, the native signal peptide sequences, both amino acid and nucleotide, described in the Reference and Sequence tables is used to modulate polypeptide transport. Further variants of the native signal peptides described in the Reference and Sequence tables are contemplated. Insertions, deletions, or substitutions can be made. Such variants retain at least one of the functions of the native signal peptide as well as exhibiting some degree of sequence identity to the native sequence.

Also, fragments of the signal peptides of the invention are useful and are fused with other signal peptides of interest to modulate transport of a polypeptide.

V. Transformation Techniques

A wide range of techniques for inserting exogenous polynucleotides are known for a number of host cells, including, without limitation, bacterial, yeast, mammalian, insect and plant cells. Techniques for transforming a wide variety of higher plant species are well known and described in the technical and scientific literature. See, e.g. Weising et al., Ann. Rev. Genet. 22:421 (1988); and Christou, Euphytica, v. 85, n.1-3:13-27, (1995).

DNA constructs of the invention are introduced into the genome of the desired plant host by a variety of conventional techniques. For example, the DNA construct is introduced directly into the genomic DNA of the plant cell using techniques such as electroporation and microinjection of plant cell protoplasts, or the DNA constructs are introduced directly to plant tissue using ballistic methods, such as DNA particle bombardment. Alternatively, the DNA constructs are combined with suitable T-DNA flanking regions and introduced into a conventional Agrobacterium tumefaciens host vector. The virulence functions of the Agrobacterium tumefaciens host will direct the insertion of the construct and adjacent marker into the plant cell DNA when the cell is infected by the bacteria (McCormac et al., Mol. Biotechnol. 8:199 (1997); Hamilton, Gene 200:107 (1997); Salomon et al. EMBO J. 3:141 (1984); Herrera-Estrella et al. EMBO J. 2:987 (1983)).

Microinjection techniques are known in the art and are described in the scientific and patent literature. The introduction of DNA constructs using polyethylene glycol precipitation is described in Paszkowski et al. EMBO J. 3:2717 (1984). Electroporation techniques are described in Fromm et al. Proc. Natl. Acad. Sci. USA 82:5824 (1985). Ballistic transformation techniques are described in Klein et al. Nature 327:773 (1987). Agrobacterium tumefaciens-mediated transformation techniques, including disarming and use of binary or co-integrate vectors, are well described in the scientific literature. See, for example Hamilton, C M., Gene 200:107 (1997); Müller et al. Mol. Gen. Genet. 207:171 (1987); Komari et al. Plant J. 10:165 (1996); Venkateswarlu et al. Biotechnology 9:1103 (1991) and Gleave, A P., Plant Mol. Biol. 20:1203 (1992); Graves and Goldman, Plant Mol. Biol. 7:34 (1986) and Gould et al., Plant Physiology 95:426 (1991).

Transformed plant cells which are derived by any of the above transformation techniques are cultured to regenerate a whole plant that possesses the transformed genotype and thus the desired phenotype, for example seedlessness. Such regeneration techniques rely on manipulation of certain phytohormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker which has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in Evans et al., Protoplasts Isolation and Culture in “Handbook of Plant Cell Culture,” pp. 124-176, MacMillan Publishing Company, New York, 1983; and Binding, Regeneration of Plants, Plant Protoplasts, pp. 21-73, CRC Press, Boca Raton, 1988. Regeneration is also obtained from plant callus, explants, organs, or parts thereof. Such regeneration techniques are described generally in Klee et al. Ann. Rev. of Plant Phys. 38:467 (1987). Regeneration of monocots (rice) is described by Hosoyama et al. (Biosci. Biotechnol. Biochem. 58:1500 (1994)) and by Ghosh et al. (J. Biotechnol. 32:1 (1994)). The nucleic acids of the invention are used to confer desired traits on essentially any plant.

Thus, the invention has use over a broad range of plants, including species from the genera Anacardium, Arachis, Asparagus, Atropa, Avena, Brassica, Citrus, Citrullus, Capsicum, Carthamus, Cocos, Coffea, Cucumis, Cucurbita, Daucus, Elaeis, Fragaria, Glycine, Gossypium, Helianthus, Heterocallis, Hordeum, Hyoscyamus, Lactuca, Linum, Lolium, Lupinus, Lycopersicon, Malus, Manihot, Majorana, Medicago, Nicotiana, Olea, Oryza, Panieum, Pannesetum, Persea, Phaseolus, Pistachia, Pisum, Pyrus, Prunus, Raphanus, Ricinus, Secale, Senecio, Sinapis, Solanum, Sorghum, Theobromus, Trigonella, Triticum, Vicia, Vitis, Vigna, and, Zea.

One of skill recognizes that after the expression cassette is stably incorporated in transgenic plants and confirmed to be operable, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques are used, depending upon the species to be crossed.

The particular sequences of SDFs identified are provided in the attached Reference and Sequence tables.

VIII. Definitions

The following terms are utilized throughout this application:

Allelic variant: An “allelic variant” is an alternative form of the same SDF, which resides at the same chromosomal locus in the organism. Allelic variations can occur in any portion of the gene sequence, including regulatory regions. Allelic variants can arise by normal genetic variation in a population. Allelic variants can also be produced by genetic engineering methods. An allelic variant can be one that is found in a naturally occurring plant, including a cultivar or ecotype. An allelic variant may or may not give rise to a phenotypic change, and may or may not be expressed. An allele can result in a detectable change in the phenotype of the trait represented by the locus. A phenotypically silent allele can give rise to a product. Alternatively spliced messages: Within the context of the current invention, “alternatively spliced messages” refers to mature mRNAs originating from a single gene with variations in the number and/or identity of exons, introns and/or intron-exon junctions. Chimeric: The term “chimeric” is used to describe genes, as defined supra, or contructs wherein at least two of the elements of the gene or construct, such as the promoter and the coding sequence and/or other regulatory sequences and/or filler sequences and/or complements thereof, are heterologous to each other. Constitutive Promoter: Promoters referred to herein as “constitutive promoters” actively promote transcription under most, but not necessarily all, environmental conditions and states of development or cell differentiation. Examples of constitutive promoters include the cauliflower mosaic virus (CaMV) 35S transcript initiation region and the 1′ or 2′ promoter derived from T-DNA of Agrobacterium tumefaciens, and other transcription initiation regions from various plant genes, such as the maize ubiquitin-1 promoter, known to those of skill. Coordinately Expressed: The term “coordinately expressed,” as used in the current invention, refers to genes that are expressed at the same or a similar time and/or stage and/or under the same or similar environmental conditions. Domain: Domains are fingerprints or signatures that can be used to characterize protein families and/or parts of proteins. Such fingerprints or signatures can comprise conserved (1) primary sequence, (2) secondary structure, and/or (3) three-dimensional conformation. Generally, each domain has been associated with either a family of proteins or motifs. Typically, these families and/or motifs have been correlated with specific in-vitro and/or in-vivo activities. A domain can be any length, including the entirety of the sequence of a protein. Detailed descriptions of the domains, associated families and motifs, and correlated activities of the polypeptides of the instant invention are described below. Usually, the polypeptides with designated domain(s) can exhibit at least one activity that is exhibited by any polypeptide that comprises the same domain(s). Endogenous: The term “endogenous,” within the context of the current invention refers to any polynucleotide, polypeptide or protein sequence which is a natural part of a cell or organisms regenerated from said cell. Exogenous: “Exogenous,” as referred to within, is any polynucleotide, polypeptide or protein sequence, whether chimeric or not, that is initially or subsequently introduced into the genome of an individual host cell or the organism regenerated from said host cell by any means other than by a sexual cross. Examples of means by which this can be accomplished are described below, and include Agrobacterium-mediated transformation (of dicots—e.g. Salomon et al. EMBO J. 3:141 (1984); Herrera-Estrella et al. EMBO J. 2:987 (1983); of monocots, representative papers are those by Escudero et al., Plant J. 10:355 (1996), Ishida et al., Nature Biotechnology 14:745 (1996), May et al., Bio/Technology 13:486 (1995)), biolistic methods (Armaleo et al., Current Genetics 17:97 1990)), electroporation, in planta techniques, and the like. Such a plant containing the exogenous nucleic acid is referred to here as a T₀ for the primary transgenic plant and T₁ for the first generation. The term “exogenous” as used herein is also intended to encompass inserting a naturally found element into a non-naturally found location. Filler sequence: As used herein, “filler sequence” refers to any nucleotide sequence that is inserted into DNA construct to evoke a particular spacing between particular components such as a promoter and a coding region and may provide an additional attribute such as a restriction enzyme site. Gene: The term “gene,” as used in the context of the current invention, encompasses all regulatory and coding sequence contiguously associated with a single hereditary unit with a genetic function (see SCHEMATIC 1). Genes can include non-coding sequences that modulate the genetic function that include, but are not limited to, those that specify polyadenylation, transcriptional regulation, DNA conformation, chromatin conformation, extent and position of base methylation and binding sites of proteins that control all of these. Genes comprised of “exons” (coding sequences), which may be interrupted by “introns” (non-coding sequences), encode proteins. A gene's genetic function may require only RNA expression or protein production, or may only require binding of proteins and/or nucleic acids without associated expression. In certain cases, genes adjacent to one another may share sequence in such a way that one gene will overlap the other. A gene can be found within the genome of an organism, artificial chromosome, plasmid, vector, etc., or as a separate isolated entity. Gene Family: “Gene family” is used in the current invention to describe a group of functionally related genes, each of which encodes a separate protein. Heterologous sequences: “Heterologous sequences” are those that are not operatively linked or are not contiguous to each other in nature. For example, a promoter from corn is considered heterologous to an Arabidopsis coding region sequence. Also, a promoter from a gene encoding a growth factor from corn is considered heterologous to a sequence encoding the corn receptor for the growth factor. Regulatory element sequences, such as UTRs or 3′ end termination sequences that do not originate in nature from the same gene as the coding sequence originates from, are considered heterologous to said coding sequence. Elements operatively linked in nature and -contiguous to each other are not heterologous to each other. On the other hand, these same elements remain operatively linked but become heterologous if other filler sequence is placed between them. Thus, the promoter and coding sequences of a corn gene expressing an amino acid transporter are not heterologous to each other, but the promoter and coding sequence of a corn gene operatively linked in a novel manner are heterologous. Homologous gene: In the current invention, “homologous gene” refers to a gene that shares sequence similarity with the gene of interest. This similarity may be in only a fragment of the sequence and often represents a functional domain such as, examples including without limitation a DNA binding domain, a domain with tyrosine kinase activity, or the like. The functional activities of homologous genes are not necessarily the same. Inducible Promoter: An “inducible promoter” in the context of the current invention refers to a promoter which is regulated under certain conditions, such as light, chemical concentration, protein concentration, conditions in an organism, cell, or organelle, etc. A typical example of an inducible promoter, which can be utilized with the polynucleotides of the present invention, is PARSK1, the promoter from the Arabidopsis gene encoding a serine-threonine kinase enzyme, and which promoter is induced by dehydration, abscissic acid and sodium chloride (Wang and Goodman, Plant J. 8:37 (1995)) Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions, elevated temperature, or the presence of light. Intergenic region: “Intergenic region,” as used in the current invention, refers to nucleotide sequence occurring in the genome that separates adjacent genes. Mutant gene: In the current invention, “mutant” refers to a heritable change in DNA sequence at a specific location. Mutants of the current invention may or may not have an associated identifiable function when the mutant gene is transcribed. Orthologous Gene: In the current invention “orthologous gene” refers to a second gene that encodes a gene product that performs a similar function as the product of a first gene. The orthologous gene may also have a degree of sequence similarity to the first gene. The orthologous gene may encode a polypeptide that exhibits a degree of sequence similarity to a polypeptide corresponding to a first gene. The sequence similarity can be found within a functional domain or along the entire length of the coding sequence of the genes and/or their corresponding polypeptides.

Percentage of sequence identity: “Percentage of sequence identity,” as used herein, is determined by comparing two optimally aligned sequences over a comparison window, where the fragment of the polynucleotide or amino acid sequence in the comparison window may comprise additions or deletions (e.g., gaps or overhangs) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Add. APL. Math. 2:482 (1981), by the homology alignment algorithm of Needleman and Wunsch J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson and Lipman Proc. Natl. Acad. Sci. (USA) 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, PASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection. Given that two sequences have been identified for comparison, GAP and BESTFIT are preferably employed to determine their optimal alignment. Typically, the default values of 5.00 for gap weight and 0.30 for gap weight length are used. The term “substantial sequence identity” between polynucleotide or polypeptide sequences refers to polynucleotide or polypeptide comprising a sequence that has at least 80% sequence identity, preferably at least 85%, more preferably at least 90% and most preferably at least 95%, even more preferably, at least 96%, 97%, 98% or 99% sequence identity compared to a reference sequence using the programs.

Plant Promoter: A “plant promoter” is a promoter capable of initiating transcription in plant cells and can drive or facilitate transcription of a fragment of the SDF of the instant invention or a coding sequence of the SDF of the instant invention. Such promoters need not be of plant origin. For example, promoters derived from plant viruses, such as the CaMV35S promoter or from Agrobacterium tumefaciens such as the T-DNA promoters, can be plant promoters. A typical example of a plant promoter of plant origin is the maize ubiquitin-1 (ubi-1)promoter known to those of skill. Promoter: The term “promoter,” as used herein, refers to a region of sequence determinants located upstream from the start of transcription of a gene and which are involved in recognition and binding of RNA polymerase and other proteins to initiate and modulate transcription. A basal promoter is the minimal sequence necessary for assembly of a transcription complex required for transcription initiation. Basal promoters frequently include a “TATA box” element usually located between 15 and 35 nucleotides upstream from the site of initiation of transcription. Basal promoters also sometimes include a “CCAAT box” element (typically a sequence CCAAT) and/or a GGGCG sequence, usually located between 40 and 200 nucleotides, preferably 60 to 120 nucleotides, upstream from the start site of transcription. Public sequence: The term “public sequence,” as used in the context of the instant application, refers to any sequence that has been deposited in a publicly accessible database. This term encompasses both amino acid and nucleotide sequences. Such sequences are publicly accessible, for example, on the BLAST databases on the NCBI FTP web site (accessible via the internet). The database at the NCBI GTP site utilizes “gi” numbers assigned by NCBI as a unique identifier for each sequence in the databases, thereby providing a non-redundant database for sequence from various databases, including GenBank, EMBL, DBBJ, (DNA Database of Japan) and PDB (Brookhaven Protein Data Bank). Regulatory Sequence: The term “regulatory sequence,” as used in the current invention, refers to any nucleotide sequence that influences transcription or translation initiation and rate, and stability and/or mobility of the transcript or polypeptide product. Regulatory sequences include, but are not limited to, promoters, promoter control elements, protein binding sequences, 5′ and 3′ UTRs, transcriptional start site, termination sequence, polyadenylation sequence, introns, certain sequences within a coding sequence, etc. Related Sequences: “Related sequences” refer to either a polypeptide or a nucleotide sequence that exhibits some degree of sequence similarity with a sequence described by The Reference tables and The Sequence tables. Scaffold Attachment Region (SAR): As used herein, “scaffold attachment region” is a DNA sequence that anchors chromatin to the nuclear matrix or scaffold to generate loop domains that can have either a transcriptionally active or inactive structure (Spiker and Thompson (1996) Plant Physiol. 110: 15-21). Sequence-determined DNA fragments (SDFs): “Sequence-determined DNA fragments” as used in the current invention are isolated sequences of genes, fragments of genes, intergenic regions or contiguous DNA from plant genomic DNA or cDNA or RNA the sequence of which has been determined. Signal Peptide: A “signal peptide” as used in the current invention is an amino acid sequence that targets the protein for secretion, for transport to an intracellular compartment or organelle or for incorporation into a membrane. Signal peptides are indicated in the tables and a more detailed description located below. Specific Promoter: In the context of the current invention, “specific promoters” refers to a subset of inducible promoters that have a high preference for being induced in a specific tissue or cell and/or at a specific time during development of an organism. By “high preference” is meant at least 3-fold, preferably at least 5-fold, more preferably at least 10-fold still more preferably at least 20-fold, 50-fold or 100-fold increase in transcription in the desired tissue over the transcription in any other tissue. Typical examples of temporal and/or tissue specific promoters of plant origin that can be used with the polynucleotides of the present invention, are: PTA29, a promoter which is capable of driving gene transcription specifically in tapetum and only during anther development (Koltonow et al., Plant Cell 2:1201 (1990); RCc2 and RCc3, promoters that direct root-specific gene transcription in rice (Xu et al., Plant Mol. Biol. 27:237 (1995); TobRB27, a root-specific promoter from tobacco (Yamamoto et al., Plant Cell 3:371 (1991)). Examples of tissue-specific promoters under developmental control include promoters that initiate transcription only in certain tissues or organs, such as root, ovule, fruit, seeds, or flowers. Other suitable promoters include those from genes encoding storage proteins or the lipid body membrane protein, oleosin. A few root-specific promoters are noted above. Stringency: “Stringency” as used herein is a function of probe length, probe composition (G+C content), and salt concentration, organic solvent concentration, and temperature of hybridization or wash conditions. Stringency is typically compared by the parameter T_(m), which is the temperature at which 50% of the complementary molecules in the hybridization are hybridized, in terms of a temperature differential from T_(m). High stringency conditions are those providing a condition of T_(m)−5° C. to T_(m)−10° C. Medium or moderate stringency conditions are those providing T_(m)−20° C. to T_(m)−29° C. Low stringency conditions are those providing a condition of T_(m)−40° C. to T_(m)−48° C. The relationship of hybridization conditions to T_(m) (in ° C.) is expressed in the mathematical equation

T _(m)=81.5−16.6(log₁₀[Na⁺])+0.41(%G+C)−(600/N)  (1)

where N is the length of the probe. This equation works well for probes 14 to 70 nucleotides in length that are identical to the target sequence. The equation below for T_(m) of DNA-DNA hybrids is useful for probes in the range of 50 to greater than 500 nucleotides, and for conditions that include an organic solvent (formamide).

T _(m)=81.5+16.6 log {[Na⁺]/(1+0.7[Na⁺])}+0.41(%G+C)−500/L 0.63(% formamide)  (2)

where L is the length of the probe in the hybrid. (P. Tijessen, “Hybridization with Nucleic Acid Probes” in Laboratory Techniques in Biochemistry and Molecular Biology, P. C. vand der Vliet, ed., c. 1993 by Elsevier, Amsterdam.) The T_(m) of equation (2) is affected by the nature of the hybrid; for DNA-RNA hybrids T_(m) is 10-15° C. higher than calculated, for RNA-RNA hybrids T_(m) is 20-25° C. higher. Because the T_(m) decreases about 1° C. for each 1% decrease in homology when a long probe is used (Bonner et al., J. Mol. Biol. 81:123 (1973)), stringency conditions can be adjusted to favor detection of identical genes or related family members.

Equation (2) is derived assuming equilibrium and therefore, hybridizations according to the present invention are most preferably performed under conditions of probe excess and for sufficient time to achieve equilibrium. The time required to reach equilibrium can be shortened by inclusion of a hybridization accelerator such as dextran sulfate or another high volume polymer in the hybridization buffer.

Stringency can be controlled during the hybridization reaction or after hybridization has occurred by altering the salt and temperature conditions of the wash solutions used. The formulas shown above are equally valid when used to compute the stringency of a wash solution. Preferred wash solution stringencies lie within the ranges stated above; high stringency is 5-8° C. below T_(m), medium or moderate stringency is 26-29° C. below T_(m) and low stringency is 45-48° C. below T_(m).

Substantially free of: A composition containing A is “substantially free of” B when at least 85% by weight of the total A+B in the composition is A. Preferably, A comprises at least about 90% by weight of the total of A+B in the composition, more preferably at least about 95% or even 99% by weight. For example, a plant gene or DNA sequence can be considered substantially free of other plant genes or DNA sequences. Translational start site: In the context of the current invention, a “translational start site” is usually an ATG in the cDNA transcript, more usually the first ATG. A single cDNA, however, may have multiple translational start sites. Transcription start site: “Transcription start site” is used in the current invention to describe the point at which transcription is initiated. This point is typically located about 25 nucleotides downstream from a TFIID binding site, such as a TATA box. Transcription can initiate at one or more sites within the gene, and a single gene may have multiple transcriptional start sites, some of which may be specific for transcription in a particular cell-type or tissue. Untranslated region (UTR): A “UTR” is any contiguous series of nucleotide bases that is transcribed, but is not translated. These untranslated regions may be associated with particular functions such as increasing mRNA message stability. Examples of UTRs include, but are not limited to polyadenylation signals, terminations sequences, sequences located between the transcriptional start site and the first exon (5′ UTR) and sequences located between the last exon and the end of the mRNA (3′ UTR). Variant: The term “variant” is used herein to denote a polypeptide or protein or polynucleotide molecule that differs from others of its kind in some way. For example, polypeptide and protein variants can consist of changes in amino acid sequence and/or charge and/or post-translational modifications (such as glycosylation, etc).

IX. Examples

The invention is illustrated by way of the following examples. The invention is not limited by these examples as the scope of the invention is defined solely by the claims following.

Example 1 cDNA Preparation

A number of the nucleotide sequences disclosed in the Reference and Sequence tables herein as representative of the SDFs of the invention are obtained by sequencing genomic DNA (gDNA) and/or cDNA from corn plants grown from HYBRID SEED # 35A19, purchased from Pioneer Hi-Bred International, Inc., Supply Management, P.O. Box 256, Johnston, Iowa 50131-0256.

A number of the nucleotide sequences disclosed in the Reference and Sequence tables herein as representative of the SDFs of the invention are also obtained by sequencing genomic DNA from Arabidopsis thaliana, Wassilewskija ecotype or by sequencing cDNA obtained from mRNA from such plants as described below. A. thaliana Wassilewskija is a true breeding strain. Seeds of the plant are available from the Arabidopsis Biological Resource Center at the Ohio State University, under the accession number CS2360. Seeds of this plant were deposited under the terms and conditions of the Budapest Treaty at the American Type Culture Collection, Manassas, Va. on Aug. 31, 1999, and were assigned ATCC No. PTA-595.

Other methods for cloning full-length cDNA are described, for example, by Seki et al., Plant Journal 15:707-720 (1998) “High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated Cap trapper”; Maruyama et al., Gene 138:171 (1994) “Oligo-capping a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides”; and WO 96/34981.

Tissues are, or each organ is, individually pulverized and frozen in liquid nitrogen. Next, the samples are homogenized in the presence of detergents and then centrifuged. The debris and nuclei are removed from the sample and more detergents were added to the sample. The sample is centrifuged and the debris is removed. Then the sample is applied to a 2M sucrose cushion to isolate polysomes. The RNA is isolated by treatment with detergents and proteinase K followed by ethanol precipitation and centrifugation. The polysomal RNA from the different tissues are pooled according to the following mass ratios: 15/15/1 for male inflorescences, female inflorescences and root, respectively. The pooled material is then used for cDNA synthesis by the methods described below.

Starting material for cDNA synthesis for the exemplary corn cDNA clones with sequences presented in the Reference and Sequence tables is poly(A)-containing polysomal mRNAs from inflorescences and root tissues of corn plants grown from HYBRID SEED # 35A19. Male inflorescences and female (pre- and post-fertilization) inflorescences are isolated at various stages of development. Selection for poly(A) containing polysomal RNA is done using oligo d(T) cellulose columns, as described by Cox and Goldberg, “Plant Molecular Biology: A Practical Approach”, pp. 1-35, Shaw ed., c. 1988 by IRL, Oxford. The quality and the integrity of the polyA+ RNAs are evaluated.

Starting material for cDNA synthesis for the exemplary Arabidopsis cDNA clones with sequences presented in the Reference and Sequence tables is polysomal RNA isolated from the top-most inflorescence tissues of Arabidopsis thaliana Wassilewskija (Ws.) and from roots of Arabidopsis thaliana Landsberg erecta (L. er.), also obtained from the Arabidopsis Biological Resource Center. Nine parts inflorescence to every part root is used, as measured by wet mass. Tissue is pulverized and exposed to liquid nitrogen. Next, the sample is homogenized in the presence of detergents and then centrifuged. The debris and nuclei are removed from the sample and more detergents are added to the sample. The sample is centrifuged and the debris removed and the sample applied to a 2M sucrose cushion to isolate polysomal RNA. Cox et al., “Plant Molecular Biology: A Practical Approach”, pp. 1-35, Shaw ed., c. 1988 by IRL, Oxford. The polysomal RNA is used for cDNA synthesis by the methods described below. Polysomal mRNA is then isolated as described above for corn cDNA. The quality of the RNA is assessed electrophoretically.

Following preparation of the mRNAs from various tissues as described above, selection of mRNA with intact 5′ ends and specific attachment of an oligonucleotide tag to the 5′ end of such mRNA is performed using either a chemical or enzymatic approach. Both techniques take advantage of the presence of the “cap” structure, which characterizes the 5′ end of most intact mRNAs and which comprises a guanosine generally methylated once, at the 7 position.

The chemical modification approach involves the optional elimination of the 2′,3′-cis diol of the 3′ terminal ribose, the oxidation of the 2′,3′-cis diol of the ribose linked to the cap of the 5′ ends of the mRNAs into a dialdehyde, and the coupling of the such obtained dialdehyde to a derivatized oligonucleotide tag. Further detail regarding the chemical approaches for obtaining mRNAs having intact 5′ ends is disclosed in International Application No. WO96/34981 published Nov. 7, 1996.

The enzymatic approach for ligating the oligonucleotide tag to the intact 5′ ends of mRNAs involves the removal of the phosphate groups present on the 5′ ends of uncapped incomplete mRNAs, the subsequent decapping of mRNAs having intact 5′ ends and the ligation of the phosphate present at the 5′ end of the decapped mRNA to an oligonucleotide tag. Further detail regarding the enzymatic approaches for obtaining mRNAs having intact 5′ ends is disclosed in Dumas Milne Edwards J. B. (Doctoral Thesis of Paris VI University, Le clonage des ADNc complets: difficultés et perspectives nouvelles. Apports pour l'étude de la régulation de l'expression de la tryptophane hydroxylase de rat, 20 Dec. 1993), EP0 625572 and Kato et al., Gene 150:243-250 (1994).

In both the chemical and the enzymatic approach, the oligonucleotide tag has a restriction enzyme site (e.g. an EcoRI site) therein to facilitate later cloning procedures. Following attachment of the oligonucleotide tag to the mRNA, the integrity of the mRNA is examined by performing a Northern blot using a probe complementary to the oligonucleotide tag.

For the mRNAs joined to oligonucleotide tags using either the chemical or the enzymatic method, first strand cDNA synthesis is performed using an oligo-dT primer with reverse transcriptase. This oligo-dT primer contains an internal tag of at least 4 nucleotides, which can be different from one mRNA preparation to another. Methylated dCTP is used for cDNA first strand synthesis to protect the internal EcoRI sites from digestion during subsequent steps. The first strand cDNA is precipitated using isopropanol after removal of RNA by alkaline hydrolysis to eliminate residual primers.

Second strand cDNA synthesis is conducted using a DNA polymerase, such as Klenow fragment and a primer corresponding to the 5′ end of the ligated oligonucleotide. The primer is typically 20-25 bases in length. Methylated dCTP is used for second strand synthesis in order to protect internal EcoRI sites in the cDNA from digestion during the cloning process.

Following second strand synthesis, the full-length cDNAs are cloned into a phagemid vector, such as pBlueScript™ (Stratagene). The ends of the full-length cDNAs are blunted with T4 DNA polymerase (Biolabs) and the cDNA is digested with EcoRI. Since methylated dCTP is used during cDNA synthesis, the EcoRI site present in the tag is the only hemi-methylated site; hence the only site susceptible to EcoRI digestion. In some instances, to facilitate subcloning, an Hind III adapter is added to the 3′ end of full-length cDNAs.

The full-length cDNAs are then size fractionated using either exclusion chromatography (AcA, Biosepra) or electrophoretic separation which yields 3 to 6 different fractions. The full-length cDNAs are then directionally cloned either into pBlueScript™ using either the EcoRI and SmaI restriction sites or, when the Hind III adapter is present in the full-length cDNAs, the EcoRI and Hind III restriction sites. The ligation mixture is transformed, preferably by electroporation, into bacteria, which are then propagated under appropriate antibiotic selection.

Clones containing the oligonucleotide tag attached to full-length cDNAs are selected as follows.

The plasmid cDNA libraries made as described above are purified (e.g. by a column available from Qiagen). A positive selection of the tagged clones is performed as follows. Briefly, in this selection procedure, the plasmid DNA is converted to single stranded DNA using phage F1 gene II endonuclease in combination with an exonuclease (Chang et al., Gene 127:95 (1993)) such as exonuclease III or T7 gene 6 exonuclease. The resulting single stranded DNA is then purified using paramagnetic beads as described by Fry et al., Biotechniques 13: 124 (1992). Here the single stranded DNA is hybridized with a biotinylated oligonucleotide having a sequence corresponding to the 3′ end of the oligonucleotide tag. Preferably, the primer has a length of 20-25 bases. Clones including a sequence complementary to the biotinylated oligonucleotide are selected by incubation with streptavidin coated magnetic beads followed by magnetic capture. After capture of the positive clones, the plasmid DNA is released from the magnetic beads and converted into double stranded DNA using a DNA polymerase such as ThermoSequenase™ (obtained from Amersham Pharmacia Biotech). Alternatively, protocols such as the Gene Trapper™ kit (Gibco BRL) can be used. The double stranded DNA is then transformed, preferably by electroporation, into bacteria. The percentage of positive clones having the 5′ tag oligonucleotide is typically estimated to be between 90 and 98% from dot blot analysis.

Following transformation, the libraries are ordered in microtiter plates and sequenced. The Arabidopsis library was deposited at the American Type Culture Collection on Jan. 7, 2000 as “E. coli liba 010600” under the accession number PTA-161.

A. Example 2 Southern Hybridizations

The SDFs of the invention are used in Southern hybridizations as described above. The following describes extraction of DNA from nuclei of plant cells, digestion of the nuclear DNA and separation by length, transfer of the separated fragments to membranes, preparation of probes for hybridization, hybridization and detection of the hybridized probe.

The procedures described herein are used to isolate related polynucleotides or for diagnostic purposes. Moderate stringency hybridization conditions, as defined above, are described in the present example. These conditions result in detection of hybridization between sequences having at least 70% sequence identity. As described above, the hybridization and wash conditions can be changed to reflect the desired percentage of sequence identity between probe and target sequences that can be detected.

In the following procedure, a probe for hybridization is produced from two PCR reactions using two primers from genomic sequence of Arabidopsis thaliana. As described above, the particular template for generating the probe can be any desired template.

The first PCR product is assessed to validate the size of the primer to assure it is of the expected size. Then the product of the first PCR is used as a template, with the same pair of primers used in the first PCR, in a second PCR that produces a labeled product used as the probe.

Fragments detected by hybridization, or other bands of interest, are isolated from gels used to separate genomic DNA fragments by known methods for further purification and/or characterization.

Buffers for Nuclear DNA Extraction 1. 10×HB

1000 ml 40 mM spermidine 10.2 g Spermine (Sigma S-2876) and spermidine (Sigma S-2501) 10 mM spermine  3.5 g Stabilize chromatin and the nuclear membrane 0.1 M EDTA 37.2 g EDTA inhibits nuclease (disodium) 0.1 M Tris 12.1 g Buffer 0.8 M KCl 59.6 g Adjusts ionic strength for stability of nuclei

-   -   Adjust pH to 9.5 with 10 N NaOH. It appears that there is a         nuclease present in leaves. Use of pH 9.5 appears to inactivate         this nuclease.         2. 2 M sucrose (684 g per 1000 ml)     -   Heat about half the final volume of water to about 50° C. Add         the sucrose slowly then bring the mixture to close to final         volume; stir constantly until it has dissolved. Bring the         solution to volume.         3. Sarkosyl solution (lyses nuclear membranes)

1000 ml N-lauroyl sarcosine (Sarkosyl) 20.0 g 0.1 M Tris 12.1 g 0.04 M EDTA (Disodium) 14.9 g

-   -   Adjust the pH to 9.5 after all the components are dissolved and         bring up to the proper volume.

4.20% Triton X-100

-   -   80 ml Triton X-100     -   320 ml 1×HB (w/o β-ME and PMSF)     -   Prepare in advance; Triton takes some time to dissolve

A. Procedure

-   1. Prepare 1×“H” buffer (keep ice-cold during use)

1000 ml 10X HB 100 ml 2 M sucrose 250 ml a non-ionic osmoticum Water 634 ml Added just before use: 100 mM PMSF*  10 ml a protease inhibitor; protects nuclear membrane proteins β-mercaptoethanol  1 ml inactivates nuclease by reducing disulfide bonds *100 mM PMSF (phenyl methyl sulfonyl fluoride, Sigma P-7626) (add 0.0875 g to 5 ml 100% ethanol)

-   2. Homogenize the tissue in a blender (use 300-400 ml of 1×HB per     blender). Be sure that you use 5-10 ml of HB buffer per gram of     tissue. Blenders generate heat so be sure to keep the homogenate     cold. It is necessary to put the blender in ice periodically. -   3. Add the 20% Triton X-100 (25 ml per liter of homogenate) and     gently stir on ice for 20 min. This lyses plastid, but not nuclear,     membranes. -   4. Filter the tissue suspension through several nylon filters into     an ice-cold beaker. The first filtration is through a 250-micron     membrane; the second is through an 85-micron membrane; the third is     through a 50-micron membrane; and the fourth is through a 20-micron     membrane. Use a large funnel to hold the filters. Filtration can be     sped up by gently squeezing the liquid through the filters. -   5. Centrifuge the filtrate at 1200×g for 20 min. at 4° C. to pellet     the nuclei. -   6. Discard the dark green supernatant. The pellet will have several     layers to it. One is starch; it is white and gritty. The nuclei are     gray and soft. In the early steps, there may be a dark green and     somewhat viscous layer of chloroplasts.     -   Wash the pellets in about 25 ml cold H buffer (with Triton         X-100) and resuspend by swirling gently and pipetting. After the         pellets are resuspended pellet the nuclei again at 1200-1300×g.         Discard the supernatant.     -   Repeat the wash 3-4 times until the supernatant has changed from         a dark green to a pale green. This usually happens after 3 or 4         resuspensions. At this point, the pellet is typically grayish         white and very slippery. The Triton X-100 in these repeated         steps helps to destroy the chloroplasts and mitochondria that         contaminate the prep.     -   Resuspend the nuclei for a final time in a total of 15 ml of H         buffer and transfer the suspension to a sterile 125 ml         Erlenmeyer flask. -   7. Add 15 ml, dropwise, cold 2% Sarkosyl, 0.1 M Tris, 0.04 M EDTA     solution (pH 9.5) while swirling gently. This lyses the nuclei. The     solution will become very viscous. -   8. Add 30 grams of CsCl and gently swirl at room temperature until     the CsCl is in solution. The mixture will be gray, white and     viscous. -   9. Centrifuge the solution at 11,400×g at 4° C. for at least 30 min.     The longer this spin is, the firmer the protein pellicle. -   10. The result is typically a clear green supernatant over a white     pellet, and (perhaps) under a protein pellicle. Carefully remove the     solution under the protein pellicle and above the pellet. Determine     the density of the solution by weighing 1 ml of solution and add     CsCl if necessary to bring to 1.57 g/ml. The solution contains     dissolved solids (sucrose etc) and the refractive index alone will     not be an accurate guide to CsCl concentration. -   11. Add 20 μl of 10 mg/ml EtBr per ml of solution. -   12. Centrifuge at 184,000×g for 16 to 20 hours in a fixed-angle     rotor. -   13. Remove the dark red supernatant that is at the top of the tube     with a plastic transfer pipette and discard. Carefully remove the     DNA band with another transfer pipette. The DNA band is usually     visible in room light; otherwise, use a long wave UV light to locate     the band. -   14. Extract the ethidium bromide (EtBr) with isopropanol saturated     with water and salt. Once the solution is clear, extract at least     two more times to ensure that all of the EtBr is gone. Be very     gentle, as it is very easy to shear the DNA at this step. This     extraction may take a while because the DNA solution tends to be     very viscous. If the solution is too viscous, dilute it with TE. -   15. Dialyze the DNA for at least two days against several changes     (at least three times) of TE (10 mM Tris, 1 mM EDTA, pH 8) to remove     the cesium chloride. -   16. Remove the dialyzed DNA from the tubing. If the dialyzed DNA     solution contains a lot of debris, centrifuge the DNA solution at     least at 2500×g for 10 min. and carefully transfer the clear     supernatant to a new tube. Read the A260 concentration of the DNA. -   17. Assess the quality of the DNA by agarose gel electrophoresis (1%     agarose gel) of the DNA. Load 50 ng and 100 ng (based on the OD     reading) and compare it with known and good quality DNA. Undigested     lambda DNA and a lambda-HindIII-digested DNA are good molecular     weight makers.

Protocol for Digestion of Genomic DNA Protocol:

-   1. The relative amounts of DNA for different crop plants that     provide approximately a balanced number of genome equivalent is     given in Table 3 below. Note that due to the size of the wheat     genome, wheat DNA will be underrepresented. Lambda DNA provides a     useful control for complete digestion. -   2. Precipitate the DNA by adding 3 volumes of 100% ethanol. Incubate     at −20° C. for at least two hours. Yeast DNA can be purchased and     made up at the necessary concentration, therefore no precipitation     is necessary for yeast DNA. -   3. Centrifuge the solution at 11,400×g for 20 min. Decant the     ethanol carefully (be careful not to disturb the pellet). Be sure     that the residual ethanol is completely removed either by vacuum     desiccation or by carefully wiping the sides of the tubes with a     clean tissue. -   4. Resuspend the pellet in an appropriate volume of water. Be sure     the pellet is fully resuspended before proceeding to the next step.     This may take about 30 min. -   5. Add the appropriate volume of 10× reaction buffer provided by the     manufacturer of the restriction enzyme to the resuspended DNA     followed by the appropriate volume of enzymes. Be sure to mix it     properly by slowly swirling the tubes. -   6. Set-up the lambda digestion-control for each DNA that you are     digesting. -   7. Incubate both the experimental and lambda digests overnight at     37° C. Spin down condensation in a microfuge before proceeding. -   8. After digestion, add 2 μl of loading dye (typically 0.25%     bromophenol blue, 0.25% xylene cyanol in 15% Ficoll or 30% glycerol)     to the lambda-control digests and load in 1% TPE-agarose gel (TPE is     90 mM Tris-phosphate, 2 mM EDTA, pH 8). If the lambda DNA in the     lambda control digests are completely digested, proceed with the     precipitation of the genomic DNA in the digests. -   9. Precipitate the digested DNA by adding 3 volumes of 100% ethanol     and incubating in—⁻20° C. for at least 2 hours (preferably     overnight).     -   EXCEPTION: Arabidopsis and yeast DNA are digested in an         appropriate volume; they don't have to be precipitated. -   10. Resuspend the DNA in an appropriate volume of TE (e.g., 22 μl×50     blots=1100 μl) and an appropriate volume of 10× loading dye (e.g.,     2.4 μl×50 blots=120 μl). Be careful in pipetting the loading dye—it     is viscous. Be sure you are pipetting the correct volume.

TABLE 3 Some guide points in digesting genomic DNA. Genome Size Equivalent Amount Relative to to 2 μg of DNA Species Genome Size Arabidopsis Arabidopsis DNA per blot Arabidopsis 120 Mb 1X   1X    2 μg Brassica 1,100 Mb 9.2X 0.54X 10 μg Corn 2,800 Mb 23.3X  0.43X 20 μg Cotton 2,300 Mb 19.2X  0.52X 20 μg Oat 11,300 Mb 94X   0.11X 20 μg Rice 400 Mb 3.3X 0.75X  5 μg Soybean 1,100 Mb 9.2X 0.54X 10 μg Sugarbeet 758 Mb 6.3X 0.8X  10 μg Sweetclover 1,100 Mb 9.2X 0.54X 10 μg Wheat 16,000 Mb 133X    0.08X 20 μg Yeast 15 Mb  0.12X 1X   0.25 μg  

Protocol for Southern Blot Analysis

The digested DNA samples are electrophoresed in 1% agarose gels in 1×TPE buffer. Low voltage, overnight separations are preferred. The gels are stained with EtBr and photographed.

-   1. For blotting the gels, first incubate the gel in 0.25 N HCl (with     gentle shaking) for about 15 min. -   2. Then briefly rinse with water. The DNA is denatured by 2     incubations. Incubate (with shaking) in 0.5 M NaOH in 1.5 M NaCl for     15 min. -   3. The gel is then briefly rinsed in water and neutralized by     incubating twice (with shaking) in 1.5 M Tris pH 7.5 in 1.5 M NaCl     for 15 min. -   4. A nylon membrane is prepared by soaking it in water for at least     5 min, then in 6×SSC for at least 15 min. before use. (20×SSC is     175.3 g NaCl, 88.2 g sodium citrate per liter, adjusted to pH 7.0.) -   5. The nylon membrane is placed on top of the gel and all bubbles in     between are removed.

The DNA is blotted from the gel to the membrane using an absorbent medium, such as paper toweling and 6×SCC buffer. After the transfer, the membrane may be lightly brushed with a gloved hand to remove any agarose sticking to the surface.

-   6. The DNA is then fixed to the membrane by UV crosslinking and     baking at 80° C. The membrane is stored at 4° C. until use.

B. Protocol for PCR Amplification of Genomic Fragments in Arabidopsis Amplification Procedures:

1. Mix the following in a 0.20 ml PCR tube or 96-well PCR plate:

Volume Stock Final Amount or Conc. 0.5 μl ~10 ng/μl genomic DNA¹ 5 ng 2.5 μl 10X PCR buffer 20 mM Tris, 50 mM KCl 0.75 μl 50 mM MgCl₂ 1.5 mM 1 μl 10 pmol/μl Primer 1 (Forward) 10 pmol 1 μl 10 pmol/μl Primer 2 (Reverse) 10 pmol 0.5 μl 5 mM dNTPs 0.1 mM 0.1 μl 5 units/μl Platinum Taq ™ (Life 1 units Technologies, Gaithersburg, MD) DNA Polymerase (to 25 μl) Water ¹ Arabidopsis DNA is used in the present experiment, but the procedure is a general one.

2. The template DNA is amplified using a Perkin Elmer 9700 PCR machine:

1) 94° C. for 10 min. followed by

2) 3) 4) 5 cycles: 5 cycles: 25 cycles: 94° C. - 30 sec 94° C. - 30 sec 94° C. - 30 sec 62° C. - 30 sec 58° C. - 30 sec 53° C. - 30 sec 72° C. - 3 min 72° C. - 3 min 72° C. - 3 min

5) 72° C. for 7 min. Then the reactions are stopped by chilling to 4° C.

The procedure can be adapted to a multi-well format if necessary.

Quantification and Dilution of PCR Products:

-   1. The product of the PCR is analyzed by electrophoresis in a 1%     agarose gel. A linearized plasmid DNA can be used as a     quantification standard (usually at 50, 100, 200, and 400 ng). These     will be used as references to approximate the amount of PCR     products. HindIII-digested Lambda DNA is useful as a molecular     weight marker. The gel can be run fairly quickly; e.g., at 100     volts. The standard gel is examined to determine that the size of     the PCR products is consistent with the expected size and if there     are significant extra bands or smeary products in the PCR reactions. -   2. The amounts of PCR products are estimated on the basis of the     plasmid standard. -   3. For the small number of reactions that produce extraneous bands,     a small amount of DNA from bands with the correct size can be     isolated by dipping a sterile 10-μl tip into the band while viewing     though a UV Transilluminator. The small amount of agarose gel (with     the DNA fragment) is used in the labeling reaction.

C. Protocol for PCR-Dig-Labeling of DNA Solutions:

-   -   Reagents in PCR reactions (diluted PCR products, 10×PCR Buffer,         50 mM MgCl₂, 5 U/μl Platinum Taq Polymerase, and the primers)     -   10×dNTP+DIG-1′-dUTP [1:5]: (2 mM dATP, 2 mM dCTP, 2 mM dGTP,         1.65 mM dTTP, 0.35 mM DIG-11-dUTP)     -   10×dNTP+DIG-11-dUTP [1:10]: (2 mM dATP, 2 mM dCTP, 2 mM dGTP,         1.81 mM dTTP, 0.19 mM DIG-11-dUTP)     -   10×dNTP+DIG-11-dUTP [1:15]: (2 mM dATP, 2 mM dCTP, 2 mM dGTP,         1.875 mM dTTP, 0.125 mM DIG-11-dUTP)     -   TE buffer (10 mM Tris, 1 mM EDTA, pH 8)     -   Maleate buffer: In 700 ml of deionized distilled water, dissolve         11.61 g maleic acid and 8.77 g NaCl. Add NaOH to adjust the pH         to 7.5. Bring the volume to 1 L. Stir for 15 min. and sterilize.     -   10% blocking solution: In 80 ml deionized distilled water,         dissolve 1.16 g maleic acid. Next, add NaOH to adjust the pH to         7.5. Add 10 g of the blocking reagent powder (Boehringer         Mannheim, Indianapolis, Ind., Cat. no. 1096176). Heat to 60° C.         while stirring to dissolve the powder. Adjust the volume to 100         ml with water. Stir and sterilize.     -   1% blocking solution: Dilute the 10% stock to 1% using the         maleate buffer.     -   Buffer 3 (100 mM Tris, 100 mM NaCl, 50 mM MgCl₂, pH9.5).         Prepared from autoclaved solutions of 1M Tris pH 9.5, 5 M NaCl,         and 1 M MgCl₂ in autoclaved distilled water.

Procedure:

-   1. PCR reactions are performed in 25 μl volumes containing:

PCR buffer 1X MgCl₂ 1.5 mM 10X dNTP + DIG-11-dUTP 1X (please see the note below) Platinum Taq ™ Polymerase 1 unit 10 pg probe DNA 10 pmol primer 1 Note: Use for: 10X dNTP + DIG-11-dUTP (1:5)   <1 kb 10X dNTP + DIG-11-dUTP (1:10) 1 kb to 1.8 kb 10X dNTP + DIG-11-dUTP (1:15) >1.8 kb

-   2. The PCR reaction uses the following amplification cycles:

1) 94° C. for 10 min.

2) 3) 4) 5 cycles: 5 cycles: 25 cycles: 95° C. - 30 sec 95° C. - 30 sec 95° C. - 30 sec 61° C. - 1 min 59° C. - 1 min 51° C. - 1 min 73° C. - 5 min 75° C. - 5 min 73° C. - 5 min

5) 72° C. for 8 min. The reactions are terminated by chilling to 4° C. (hold).

-   3. The products are analyzed by electrophoresis-in a 1% agarose gel,     comparing to an aliquot of the unlabelled probe starting material. -   4. The amount of DIG-labeled probe is determined as follows:     -   Make serial dilutions of the diluted control DNA in dilution         buffer (TE: 10 mM Tris and 1 mM EDTA, pH 8) as shown in the         following table:

DIG-labeled control Final Conc. DNA starting conc. Stepwise Dilution (Dilution Name)  5 ng/μl  1 μl in 49 μl TE 100 pg/μl (A) 100 pg/μl (A) 25 μl in 25 μl TE  50 pg/μl (B)  50 pg/μl (B) 25 μl in 25 μl TE  25 pg/μl (C)  25 pg/μl (C) 20 μl in 30 μl TE  10 pg/μl (D)

-   -   a. Serial deletions of a DIG-labeled standard DNA ranging from         100 pg to 10 pg are spotted onto a positively charged nylon         membrane, marking the membrane lightly with a pencil to identify         each dilution.     -   b. Serial dilutions (e.g., 1:50, 1:2500, 1:10,000) of the newly         labeled DNA probe are spotted.     -   c. The membrane is fixed by UV crosslinking.     -   d. The membrane is wetted with a small amount of maleate buffer         and then incubated in 1% blocking solution for 15 min at room         temp.     -   e. The labeled DNA is then detected using alkaline phosphatase         conjugated anti-DIG antibody (Boehringer Mannheim, Indianapolis,         Ind., cat. no. 1093274) and an NBT substrate according to the         manufacture's instruction.     -   f. Spot intensities of the control and experimental dilutions         are then compared to estimate the concentration of the         PCR-DIG-labeled probe.

D. Prehybridization and Hybridization of Southern Blots Solutions:

100% Formamide purchased from Gibco 20X SSC (1X = 0.15 M NaCl, 0.015 M Na₃citrate) per L: 175 g NaCl 87.5 g Na₃citrate•2H₂0 20% Sarkosyl (N-lauroyl-sarcosine) 20% SDS (sodium dodecyl sulphate) 10% Blocking Reagent: In 80 ml deionized distilled water, dissolve 1.16 g maleic acid. Next, add NaOH to adjust the pH to 7.5. Add 10 g of the blocking reagent powder. 60° C. while stirring to dissolve the powder. Adjust the volume to 100 ml with water. Stir and sterilize.

Prehybridization Mix:

Final Volume Concentration Components (per 100 ml) Stock   50% Formamide 50 ml 100%  5X SSC 25 ml 20X  0.1% Sarkosyl 0.5 ml  20% 0.02% SDS 0.1 ml   20%   2% Blocking Reagent 20 ml 10% Water 4.4 ml 

General Procedures:

-   1. Place the blot in a heat-sealable plastic bag and add an     appropriate volume of prehybridization solution (30 ml/100 cm²) at     room temperature. Seal the bag with a heat sealer, avoiding bubbles     as much as possible. Lay down the bags in a large plastic tray (one     tray can accommodate at least 4-5 bags). Ensure that the bags are     lying flat in the tray so that the prehybridization solution is     evenly distributed throughout the bag. Incubate the blot for at     least 2 hours with gentle agitation using a waver shaker. -   2. Denature DIG-labeled DNA probe by incubating for 10 min. at     98° C. using the PCR machine and immediately cool it to 4° C. -   3. Add probe to prehybridization solution (25 ng/ml; 30 ml=750 ng     total probe) and mix well but avoid foaming. Bubbles may lead to     background. -   4. Pour off the prehybridization solution from the hybridization     bags and add new prehybridization and probe solution mixture to the     bags containing the membrane. -   5. Incubate with gentle agitation for at least 16 hours. -   6. Proceed to medium stringency post-hybridization wash:     -   Three times for 20 min. each with gentle agitation using 1×SSC,         1% SDS at 60° C.     -   All wash solutions must be prewarmed to 60° C. Use about 100 ml         of wash solution per membrane.     -   To avoid background keep the membranes fully submerged to avoid         drying in spots; agitate sufficiently to avoid having membranes         stick to one another. -   7. After the wash, proceed to immunological detection and CSPD     development.

E. Procedure for Immunological Detection with CSPD Solutions:

Buffer 1: Maleic acid buffer (0.1 M maleic acid, 0.15 M NaCl; adjusted to pH 7.5 with NaoH) Washing buffer: Maleic acid buffer with 0.3% (v/v) Tween 20. Blocking stock 10% blocking reagent in buffer 1. Dissolve (10X solution concentration): blocking reagent powder (Boehringer Mannheim, Indianapolis, IN, cat. no. 1096176) by constantly stirring on a 65° C. heating block or heat in a microwave, autoclave and store at 4° C. Buffer 2 Dilute the stock solution 1:10 in Buffer 1. (1X blocking solution): Detection buffer: 0.1 M Tris, 0.1 M NaCl, pH 9.5

Procedure:

-   1. After the post-hybridization wash the blots are briefly rinsed     (1-5 min.) in the maleate washing buffer with gentle shaking. -   2. Then the membranes are incubated for 30 min. in Buffer 2 with     gentle shaking. -   3. Anti-DIG-AP conjugate (Boehringer Mannheim, Indianapolis, Ind.,     cat. no. 1093274) at 75 mU/ml (1:10,000) in Buffer 2 is used for     detection. 75 ml of solution can be used for 3 blots. -   4. The membrane is incubated for 30 min. in the antibody solution     with gentle shaking. -   5. The membrane are washed twice in washing buffer with gentle     shaking. About 250 mls is used per wash for 3 blots. -   6. The blots are equilibrated for 2-5 min in 60 ml detection buffer. -   7. Dilute CSPD (1:200) in detection buffer. (This can be prepared     ahead of time and stored in the dark at 4° C.).     -   The following steps must be done individually. Bags (one for         detection and one for exposure) are generally cut and ready         before doing the following steps. -   8. The blot is carefully removed from the detection buffer and     excess liquid removed without drying the membrane. The blot is     immediately placed in a bag and 1.5 ml of CSPD solution is added.     The CSPD solution can be spread over the membrane. Bubbles present     at the edge and on the surface of the blot are typically removed by     gentle rubbing. The membrane is incubated for 5 min. in CSPD     solution. -   9. Excess liquid is removed and the membrane is blotted briefly (DNA     side up) on Whatman 3MM paper. Do not let the membrane dry     completely. -   10. Seal the damp membrane in a hybridization bag and incubate for     10 min at 37° C. to enhance the luminescent reaction. -   11. Expose for 2 hours at room temperature to X-ray film. Multiple     exposures can be taken. Luminescence continues for at least 24 hours     and signal intensity increases during the first hours.

Example 3 Microarray Experiments and Results 1. Sample Tissue Preparation

(a) Abscissic acid (ABA)

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) are sown in trays and left at 4° C. for 4 days to vernalize. They are then transferred to a growth chamber having grown 16 hr light/8 hr dark, 13,000 LUX, 70% humidity, and 20° C. and watered twice a week with 1 L of 1× Hoagland's solution. Approximately 1,000 14 day old plants are sprayed with 200-250 mls of 100 μM ABA in a 0.02% solution of the detergent Silwet L-77. Whole seedlings, including roots, are harvested within a 15 to 20 minute time period at 1 hr and 6 hr after treatment, flash-frozen in liquid nitrogen and stored at ⁻80° C.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 7 days. Seedlings are carefully removed from the sand and placed in 1-liter beakers with 100 μM ABA for treatment. Control plants are treated with water. After 6 hr and 24 hr, aerial and root tissues are separated and flash frozen in liquid nitrogen prior to storage at ⁻80° C.

(b) Ap2

Seeds of Arabidopsis thaliana (ecotype Landesberg erecta) and floral mutant apetala2 (Jofuku et al., 1994, Plant Cell 6:1211-1225) are sown in pots and left at 4° C. for two to three days to vernalize. They are then transferred to a growth chamber. Plants are grown under long-day (16 hr light, 8 hr dark) conditions 7000-8000 LUX light intensity, 70% humidity and 22° C. temperature. Inflorescences containing immature floral buds (stages 1-7; Bowman, 1994) as well as the inflorescence meristem are harvested and flash frozen. Polysomal polyA+ RNA is isolated from tissue according to Cox and Goldberg, 1988).

(c) Ovules (Ler-pi)

Seeds of Arabidopsis thaliana heterozygous for pistillata (pi) (ecotype Landsberg erecta (Ler)) are sown in pots and left at 4° C. for two to three days to vernalize. They are then transferred to a growth chamber. Plants are grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 76% humidity, and 24° C. temperature. Inflorescences are harvested from seedlings about 40 days old. The inflorescences are cut into small pieces and incubated in the following enzyme solution (pH 5) at room temperature for 0.5-1 hr.: 0.2% pectolyase Y-23, 0.04% pectinase, 5 mM MES, 3% Sucrose and MS salts (1900 mg/l KNO₃, 1650 mg/l NH₄NO₃, 370 mg/l MgSO₄.7H₂O, 170 mg/l KH₂PO₄, 440 mg/l CaCl₂.2H₂O, 6.2 mg/l H₂BO₃, 15.6 mg/l MnSO₄.4H₂O, 8.6 mg/l ZnSO₄.7H₂O, 0.25 mg/l NaMoO₄.2H₂O, 0.025 mg/l CuCO₄5.H₂O, 0.025 mg/l CoCl₂.6H₂O, 0.83 mg/l KI, 27.8 mg/l FeSO₄.7H₂O, 37.3 mg/l Disodium EDTA, pH 5.8). At the end of the incubation the mixture of inflorescence material and enzyme solution is passed through a size 60 sieve and then through a sieve with a pore size of 125 μm. Ovules greater than 125 μm in diameter are collected, rinsed twice in B5 liquid medium (2500 mg/l KNO₃, 250 mg/l MgSO₄. 7H₂O, 150 mg/l NaH2PO₄.H₂O, 150 mg/l CaCl₂.2H₂O, 134 mg/l (NH4)2CaCl₂.SO₄, 3 mg/l H₂BO₃, 10 mg/l MnSO₄.4H₂O, 2ZnSO₄.7H₂O, 0.25 mg/l NaMoO₄.2H₂O, 0.025 mg/l CuCO₄.5H₂O, 0.025 mg/l CoCl₂.6H₂O, 0.75 mg/l KI, 40 mg/l EDTA sodium ferric salt, 20 g/l sucrose, 10 mg/l Thiamine hydrochloride, 1 mg/l Pyridoxine hydrochloride, 1 mg/l Nicotinic acid, 100 mg/l myoinositol, pH 5.5)), rinsed once in deionized water and flash frozen in liquid nitrogen. The supernatant from the 125 μm sieving is passed through subsequent sieves of 50 μm and 32 μm. The tissue retained in the 32 μm sieve is collected and mRNA prepared for use as a control.

(d) Brassinosteroid Responsive (Br, Bz)

Two separate experiments are performed, one with epi-brassinolide and one with the brassinosteroid biosynthetic inhibitor brassinazole.

In the epi-brassinolide experiments, seeds of wild-type Arabidopsis thaliana (ecotype Wassilewskija) and the brassinosteroid biosynthetic mutant dwf4-1 are sown in trays and left at 4° C. for 4 days to vernalize. They are then transferred to a growth chamber having 16 hr light/8 hr dark, 11,000 LUX, 70% humidity and 22° C. temperature. Four week old plants are spayed with a 1 μM solution of epi-brassinolide and shoot parts (unopened floral primordia and shoot apical meristems) harvested three hours later. Tissue is flash-frozen in liquid nitrogen and stored at ⁻80° C.

In the brassinazole experiments, seeds of wild-type Arabidopsis thaliana (ecotype Wassilewskija) are grown as described above. Four week old plants are sprayed with a 1 μM solution of brassinazole and shoot parts (unopened floral primordia and shoot apical meristems) harvested three hours later. Tissue is flash-frozen in liquid nitrogen and stored at ⁻80° C.

In addition to the spray experiments, tissue is prepared from two different mutants; (1) a dwf4-1 knock out mutant and (2) a mutant overexpressing the dwf4-1 gene

Seeds of wild-type Arabidopsis thaliana (ecotype Wassilewskija) and of the dwf4-1 knock out and overexpressor mutants are sown in trays and left at 4° C. for 4 days to vernalize. They are then transferred to a growth chamber having 16 hr light/8 hr dark, 11,000 LUX, 70% humidity and 22° C. temperature. Tissue from shoot parts (unopened floral primordia and shoot apical meristems) is flash-frozen in liquid nitrogen and stored at ⁻80° C.

Another experiment is completed with seeds of Arabidopsis thaliana (ecotype Wassilewskija) that are sown in trays and left at 4° C. for 4 days to vernalize. They are then transferred to a growth chamber. Plants are grown under long-day (16 hr light: 8 hr. dark) conditions, 13,000 LUX light intensity, 70% humidity, 20° C. temperature and watered twice a week with 1 L 1× Hoagland's solution (recipe recited in Feldmann et al., (1987) Mol. Gen. Genet. 208: 1-9 and described as complete nutrient solution). Approximately 1,000 14 day old plants are spayed with 200-250 mls of 0.1 μM Epi-Brassinolite in 0.02% solution of the detergent Silwet L-77. At 1 hr. and 6 hrs. after treatment aerial tissues are harvested within a 15 to 20 minute time period and flash-frozen in liquid nitrogen.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 7 days. Seedlings are carefully removed from the sand and placed in 1-liter beakers with 0.1 μM epi-brassinolide for treatment. Control plants are treated with distilled deionized water. After 24 hr, aerial and root tissues are separated and flash frozen in liquid nitrogen prior to storage at ⁻80° C.

(e) CS6630

Arabidopsis thaliana (ecotype Wassilewskija) seeds are vernalized at 4° C. for 3 days before sowing on MS media (1%) sucrose on bactor-agar. Roots and shoots are separated 14 days after germination, flash frozen in liquid nitrogen and stored at ⁻80° C.

(f) CS6632 Shoots-Roots

Seedlings are grown on regular MS (1% sucrose) bacto-agar. 14 day old seedlings (days after germination) roots and shoots were separated nand flash frozen in liquid N₂.

(g) Cold (8_deg)

Sterilized Arabidopsis thaliana (ecotype Wassilewskija) seeds are kept at 4° C. in dark for three days and carefully spread on 0.5×MS plates by dispersing ˜300-500 seeds on agar surface. Plates are left to dry in the hood for 15-20 min. and then sealed with micropore tape. Plates are placed in a Percival growth chamber set at 22C, 16 h light/8 h dark. By day 7 (9 AM), half of plates are moved into another Percival growth chamber whose setting is identical to the previous one except that the temperature is set to 8° C. Plants are gently pulled out from plates and harvested/frozen at 2 hrs, 4 hrs, 8 hrs, 2 days, 4 days, 7 days, 9 days and 11 days after transfer. Samples kept in the 22° C. chamber are harvested at the same time as the cold-treated samples.

(h) Cold Shock Treatment (4 deg)

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) are sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C. and 70% humidity. Fourteen day old plants are transferred to a 4° C. dark growth chamber and aerial tissues are harvested 1 hour and 6 hours later. Control plants are maintained at 20° C. and covered with foil to avoid exposure to light. Tissues are flash-frozen in liquid nitrogen and stored at ⁻80° C.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 7 days. Seedlings are carefully removed from the sand and placed in 1-liter beakers containing 4° C. water for treatment. Control plants are treated with water at 25° C. After 1 hr and 6 hr aerial and root tissues are separated and flash frozen in liquid nitrogen prior to storage at −80° C.

(i) Cytokinin (BA)

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) are sown in trays and left at 4° C. for 4 days to vernalize. They are then transferred to a growth chamber having 16 hr light/8 hr dark, 13,000 LUX, 70% humidity, 20° C. temperature and watered twice a week with 1 L of 1× Hoagland's solution. Approximately 1,000 14 day old plants are spayed with 200-250 mls of 100 μM BA in a 0.02% solution of the detergent Silwet L-77. Aerial tissues (everything above the soil line) are harvested within a 15 to 20 minute time period 1 hr and 6 hrs after treatment, flash-frozen in liquid nitrogen and stored at ⁻80° C.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings are carefully removed from the sand and placed in 1-liter beakers with 100 μM BA for treatment. Control plants are treated with water. After 6 hr, aerial and root tissues are separated and flash frozen in liquid nitrogen prior to storage at ⁻80° C.

(j) Diversity_Expt

Sterilized and wild-type Arabidopsis thaliana seeds (ecotype Wassilewskija) and wild-type Arabis holboellii seeds are sown in MS boxes (0.5% sucrose, 1.5% agar) after 3 day-cold treatment. The boxes are placed horizontally in a Percival growth chamber (16:8 light cycles, 22° C.) so that hypocotyls grow upward. The hypocotyls are harvested after 7 d in the chamber, flash-frozen in liquid nitrogen and stored at −80° C.

(j) Drought Reproduction

Arabidopsis thaliana (ecotype Wassilewskija) seeds are kept at 4° C. in dark for three days and then sown in soil mix (Metromix 200) with a regular watering schedule (1.5-2 L per flat per week). Drought treatment by withholding water starts when plants are 30-days-old. The control samples are watered as before. Rosettes, flowers (with siliques less than 5 mm) and siliques (>5 mm) are harvested separately on day 5, 7 and 10 post-drought-treatment (PDT). By day 10 PDT, the majority of drought plants are wilted and unable to recover after re-watering and the experiment is terminated. The samples are harvested between 2-5 PM. Plants are grown in a walk-in growth chamber under these conditions: 16 h light/8 hr dark, 70% relative humidity, 20° C. light/18° C. dark for the first 10 days, and under 22° C. light/20° C. dark for the following days.

(j) Drought Stress

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) are sown in pots and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 150,000-160,000 LUX, 20° C. and 70% humidity. After 14 days, aerial tissues are cut and left to dry on 3MM Whatman paper in a petri-plate for 1 hour and 6 hours. Aerial tissues exposed for 1 hour and 6 hours to 3 MM Whatman paper wetted with 1× Hoagland's solution serve as controls. Tissues are harvested, flash-frozen in liquid nitrogen and stored at −80° C.

Alternatively, Arabidopsis thaliana (ecotype Wassilewskija) seed is vernalized at 4° C. for 3 days before sowing in Metromix soil type 350. Flats are placed in a growth chamber with 23° C., 16 hr light/8 hr. dark, 80% relative humidity, ˜13,000 LUX for germination and growth. Plants are watered with 1-1.5 L of water every four days. Watering is stopped 16 days after germination for the treated samples, but continues for the control samples. Rosette leaves and stems, flowers and siliques are harvested 2 d, 3 d, 4 d, 5 d, 6 d and 7 d after watering is stopped. Tissue is flash frozen in liquid nitrogen and kept at −80° C. until RNA is isolated. Flowers and siliques are also harvested on day 8 from plants that had undergone a 7 d drought treatment followed by 1 day of watering. Control plants (whole plants) are harvested after 5 weeks, flash frozen in liquid nitrogen and stored as above.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 7 days. Seedlings are carefully removed from the sand and placed in empty 1-liter beakers at room temperature for treatment. Control plants are placed in water. After 1 hr, 6 hr, 12 hr and 24 hr aerial and root tissues are separated and flash frozen in liquid nitrogen prior to storage at ⁻80° C.

(k) Far-Red-Enriched-Adult

Wildtype Arabidopsis thaliana (ecotype Columbia) seeds are planted on soil and vernalized for 4 days at 4° C. Soil sown plants are grown in a growth room (16 h light/8 h dark, 22° C.; 4 bulbs total alternating Gro-Lux and cool whites); light measurements are as follows: Red=330.9 μW/cm², Blue=267 μW/cm², Far Red=56.1 μW/cm². At 4 weeks after germination, the soil pots are transferred to shade environment (16 h light/8 h dark; Red=376 μW/cm², Blue=266 μW/cm², Far Red=552 μW/cm²) for various durations of exposure time (1, 4, 8, 16, 24, 48, and 72 hrs). After timed exposure, above ground tissue is flash frozen with liquid nitrogen and stored at −80° C. Control seedlings are not transferred, but are collected at the same time as corresponding shade-exposed experimental samples.

(1) Far-Red-Induction

Seeds from wildtype Arabidopsis thaliana (ecotype Columbia) are vernalized in sterile water for 4 days at 4° C. prior to planting. Seeds are then sterilized and evenly planted on 0.5% sucrose MS media plates. Plates are sealed with Scotch micropore tape to allow for gas exchange and prevent contamination. Plates are grown in a growth room (16 h light/8 h dark, 22° C.; 6 bulbs total Gro-Lux); light measurements are as follows: Red=646.4 μW/cm², Blue=387 μW/cm², Far Red=158.7 μW/cm². At 7 days after germination, the plates containing the seedlings are transferred to Far Red light only (Far Red=525 μW/cm²) for various durations of exposure time (1, 4, 8, and 24 hrs). After timed exposure, tissue is flash frozen with liquid nitrogen and stored at −80° C. Control seedlings are not transferred, but are collected at same time as the corresponding far-red exposed experimental samples.

(m) Flowers (Green, White or Buds)

Approximately 10 μl of Arabidopsis thaliana seeds (ecotype Wassilewskija) are sown on 350 soil (containing 0.03% marathon) and vernalized at 4C for 3 days. Plants are then grown at room temperature under fluorescent lighting until flowering. Flowers are harvested after 28 days in three different categories. Buds that had not opened at all and are completely green are categorized as “flower buds” (also referred to as green buds by the investigator). Buds that had started to open, with white petals emerging slightly are categorized as “green flowers” (also referred to as white buds by the investigator). Flowers that are mostly opened (with no silique elongation) with white petals completely visible are categorized as “white flowers” (also referred to as open flowers by the investigator). Buds and flowers are harvested with forceps, flash frozen in liquid nitrogen and stored at ⁻80° C. until RNA is isolated.

(n) Germination

Arabidopsis thaliana seeds (ecotype Wassilewskija) is sterilized in bleach and rinsed with sterile water. The seeds are placed in 100 mm petri plates containing soaked autoclaved filter paper. Plates are foil-wrapped and left at 4° C. for 3 nights to vernalize. After cold treatment, the foil is removed and plates are placed into a growth chamber having 16 hr light/8 hr dark cycles, 23° C., 70% relative humidity and ˜11,000 lux. Seeds are collected 1 d, 2 d, 3 d and 4 d later, flash frozen in liquid nitrogen and stored at −80° C. until RNA is isolated.

(o) Guard Cells

Arabidopsis thaliana (ecotype Wassilewskija) seeds are vernalized at 4° C. for 3 days before sowing. Leaves are harvested, homogenized and centrifuged to isolate the guard cell containing fraction. Homogenate from leaves served as the control. Samples are flash frozen in liquid nitrogen and stored at −80° C. Identical experiments using leaf tissue from canola are performed.

(p) Heat Shock Treatment

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) are sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber with 16 hr light/8 hr dark, 12,000-14,000 LUX, 70% humidity and 20° C., fourteen day old plants are transferred to a 42° C. growth chamber and aerial tissues are harvested 1 hr and 6 hr after transfer. Control plants are left at 20° c. and aerial tissues are harvested. Tissues are flash-frozen in liquid nitrogen and stored at ⁻80° c.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 7 days. Seedlings are carefully removed from the sand and placed in 1-liter beakers containing 42° C. water for treatment. Control plants are treated with water at 25° C. After 1 hr and 6 hr aerial and root tissues are separated and flash frozen in liquid nitrogen prior to storage at ⁻80° C.

(q) Herbicide Treatment

Arabidopsis thaliana (ecotype Wassilewskija) seeds are sterilized for 5 min. with 30% bleach, 50 μl Triton in a total volume of 50 ml. Seeds are vernalized at 4° C. for 3 days before being plated onto GM agar plates at a density of about 144 seeds per plate. Plates are incubated in a Percival growth chamber having 16 hr light/8 hr dark, 80% relative humidity, 22° C. and 11,000 LUX for 14 days.

Plates are sprayed (˜0.5 mls/plate) with water, Finale (1.128 g/L), Glean (1.88 g/L), RoundUp (0.01 g/L) or Trimec (0.08 g/L). Tissue is collected and flash frozen in liquid nitrogen at the following time points: 0, 1, 2, 4, 8, 12, and 24 hours. Frozen tissue is stored at −80° C. prior to RNA isolation.

(r) Imbibed Seed

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in covered flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. One day after sowing, whole seeds are flash frozen in liquid nitrogen prior to storage at ⁻80° C. Two days after sowing, embryos and endosperm are isolated and flash frozen in liquid nitrogen prior to storage at −80° C. On days 3-6, aerial tissues, roots and endosperm are isolated and flash frozen in liquid nitrogen prior to storage at ⁻80° C.

(s) Interploidy Crosses

Interploidy crosses involving a 6× parent are lethal. Crosses involving a 4× parent are complete and analyzed. The imbalance in the maternal/paternal ratio produced from the cross can lead to big seeds. Arabidopsis thaliana (ecotype Wassilewskija) seeds are vernalized at 4° C. for 3 days before sowing. Small siliques are harvested at 5 days after pollination, flash frozen in liquid nitrogen and stored at −80° C.

(t) Line Comparisons

Alkaloid 35S over-expressing lines are used to monitor the expression levels of terpenoid/alkaloid biosynthetic and P450 genes to identify the transcriptional regulatory points in the biosynthesis pathway and the related P450 genes. Arabidopsis thaliana (ecotype Wassilewskija) seeds are vernalized at 4° C. for 3 days before sowing in vermiculite soil (Zonolite) supplemented by Hoagland solution. Flats are placed in Conviron growth chambers under long day conditions (16 hr light, 23° C./8 hr dark, 20° C.). Basta spray and selection of the overexpressing lines is conducted about 2 weeks after germination. Approximately 2-3 weeks after bolting (approximately 5-6 weeks after germination), aerial portions (e.g. stem and siliques) from the over-expressing lines and from wild-type plants are harvested, flash frozen in liquid nitrogen and stored at −80° C.

(u) Methyl Jasmonate (MeJ)

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) are sown in trays and left at 4° C. for 4 days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr. dark, 13,000 LUX, 70% humidity, 20° C. temperature and watered twice a week with 1 L of a 1× Hoagland's solution. Approximately 1,000 14 day old plants are sprayed with 200-250 mls of 0.001% methyl jasmonate in a 0.02% solution of the detergent Silwet L-77. At 1 hr and 6 hrs after treatment, whole seedlings, including roots, are harvested within a 15 to 20 minute time period, flash-frozen in liquid nitrogen and stored at 80° C.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 7 days. Seedlings are carefully removed from the sand and placed in 1-liter beakers with 0.001% methyl jasmonate for treatment. Control plants are treated with water. After 24 hr, aerial and root tissues are separated and flash frozen in liquid nitrogen prior to storage at ⁻80° C.

(v) Nitric Oxide Treatment (Nanp)

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) are sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C. and 70% humidity. Fourteen day old plants are sprayed with 5 mM sodium nitroprusside in a 0.02% Silwett L-77 solution. Control plants are sprayed with a 0.02% Silwett L-77 solution. Aerial tissues are harvested 1 hour and 6 hours after spraying, flash-frozen in liquid nitrogen and stored at ⁻80° C.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 7 days. Seedlings are carefully removed from the sand and placed in 1-liter beakers with 5 mM nitroprusside for treatment. Control plants are treated with water. After 1 hr, 6 hr and 12 hr, aerial and root tissues are separated and flash frozen in liquid nitrogen prior to storage at ⁻80° C.

(w) Nitrogen: Low to High

Arabidopsis thaliana (ecotype Wassilewskija) seeds are sown on flats containing 4 L of a 1:2 mixture of Grace Zonolite vermiculite and soil. Flats are watered with 3 L of water and vernalized at 4° C. for five days. Flats are placed in a Conviron growth chamber having 16 hr light/8 hr dark at 20° C., 80% humidity and 17,450 LUX. Flats are watered with approximately 1.5 L of water every four days. Mature, bolting plants (24 days after germination) are bottom treated with 2 L of either a control (100 mM mannitol pH 5.5) or an experimental (50 mM ammonium nitrate, pH 5.5) solution. Roots, leaves and siliques are harvested separately 30, 120 and 240 minutes after treatment, flash frozen in liquid nitrogen and stored at ⁻80° C.

Hybrid maize seed (Pioneer hybrid 35A19) are aerated overnight in deionized water. Thirty seeds are plated in each flat, which contained 4 liters of Grace zonolite vermiculite. Two liters of water are bottom fed and flats were kept in a Conviron growth chamber with 16 hr light/8 hr dark at 20° C. and 80% humidity. Flats are watered with 1 L of tap water every three days. Five day old seedlings are treated as described above with 2 L of either a control (100 mM mannitol pH 6.5) solution or 1 L of an experimental (50 mM ammonium nitrate, pH 6.8) solution. Fifteen shoots per time point per treatment are harvested 10, 90 and 180 minutes after treatment, flash frozen in liquid nitrogen and stored at ⁻80° C.

Alternatively, seeds of Arabidopsis thaliana (ecotype Wassilewskija) are left at 4° C. for 3 days to vernalize. They are then sown on vermiculite in a growth chamber having 16 hours light/8 hours dark, 12,000-14,000 LUX, 70% humidity, and 20° C. They are bottom-watered with tap water, twice weekly. Twenty-four days old plants are sprayed with either water (control) or 0.6% ammonium nitrate at 4 μL/cm of tray surface. Total shoots and some primary roots are cleaned of vermiculite, flash-frozen in liquid nitrogen and stored at ⁻80° C.

(x) Nitrogen High to Low

Wild type Arabidopsis thaliana seeds (ecotype Wassilewskija) are surface sterilized with 30% Clorox, 0.1% Triton X-100 for 5 minutes. Seeds are then rinsed with 4-5 exchanges of sterile double distilled deionized water. Seeds are vernalized at 4° C. for 2-4 days in darkness. After cold treatment, seeds are plated on modified 1×MS media (without NH₄NO₃ or KNO₃), 0.5% sucrose, 0.5 g/L MES pH5.7, 1% phytagar and supplemented with KNO₃ to a final concentration of 60 mM (high nitrate modified 1×MS media). Plates are then grown for 7 days in a Percival growth chamber at 22° C. with 16 hr. light/8 hr dark.

Germinated seedlings are then transferred to a sterile flask containing 50 mL of high nitrate modified 1×MS liquid media. Seedlings are grown with mild shaking for 3 additional days at 22° C. in 16 hr. light/8 hr dark (in a Percival growth chamber) on the high nitrate modified 1×MS liquid media.

After three days of growth on high nitrate modified 1×MS liquid media, seedlings are transferred either to a new sterile flask containing 50 mL of high nitrate modified 1×MS liquid media or to low nitrate modified 1×MS liquid media (containing 20 μM KNO₃). Seedlings are grown in these media conditions with mild shaking at 22° C. in 16 hr light/8 hr dark for the appropriate time points and whole seedlings harvested for total RNA isolation via the Trizol method (LifeTech.). The time points used for the microarray experiments are 10 min. and 1 hour time points for both the high and low nitrate modified 1×MS media.

Alternatively, seeds that are surface sterilized in 30% bleach containing 0.1% Triton X-100 and further rinsed in sterile water, are planted on MS agar, (0.5% sucrose) plates containing 50 mM KNO₃ (potassium nitrate). The seedlings are grown under constant light (3500 LUX) at 22° C. After 12 days, seedlings are transferred to MS agar plates containing either 1 mM KNO₃ or 50 mM KNO₃. Seedlings transferred to agar plates containing 50 mM KNO₃ are treated as controls in the experiment. Seedlings transferred to plates with 1 mM KNO₃ are rinsed thoroughly with sterile MS solution containing 1 mM KNO₃. There are ten plates per transfer. Root tissue was collected and frozen in 15 mL Falcon tubes at various time points which included 1 hour, 2 hours, 3 hours, 4 hours, 6 hours, 9 hours, 12 hours, 16 hours, and 24 hours.

Maize 35A19 Pioneer hybrid seeds are sown on flats containing sand and grown in a Conviron growth chamber at 25° C., 16 hr light/8 hr dark, ˜13,000 LUX and 80% relative humidity. Plants are watered every three days with double distilled deionized water. Germinated seedlings are allowed to grow for 10 days and are watered with high nitrate modified 1×MS liquid media (see above). On day 11, young corn seedlings are removed from the sand (with their roots intact) and rinsed briefly in high nitrate modified 1×MS liquid media. The equivalent of half a flat of seedlings is then submerged (up to their roots) in a beaker containing either 500 mL of high or low nitrate modified 1×MS liquid media (see above for details).

At appropriate time points, seedlings are removed from their respective liquid media, the roots separated from the shoots and each tissue type flash frozen in liquid nitrogen and stored at ⁻80° C. This is repeated for each time point. Total RNA is isolated using the Trizol method (see above) with root tissues only.

Corn root tissues isolated at the 4 hr and 16 hr time points are used for the microarray experiments. Both the high and low nitrate modified 1×MS media are used.

(y) Osmotic Stress (PEG)

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) are sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C., and 70% humidity. After 14 days, the aerial tissues are cut and placed on 3 MM Whatman paper in a petri-plate wetted with 20% PEG (polyethylene glycol-M_(r) 8,000) in 1× Hoagland's solution. Aerial tissues on 3 MM Whatman paper containing 1× Hoagland's solution alone serve as the control. Aerial tissues are harvested at 1 hour and 6 hours after treatment, flash-frozen in liquid nitrogen and stored at ⁻80° C.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 7 days. Seedlings are carefully removed from the sand and placed in 1-liter beakers with 20% PEG (polyethylene glycol-M_(r) 8,000) for treatment. Control plants are treated with water. After 1 hr and 6 hr aerial and root tissues are separated and flash frozen in liquid nitrogen prior to storage at ⁻80° C.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 7 days. Seedlings are carefully removed from the sand and placed in 1-liter beakers with 150 mM NaCl for treatment. Control plants were treated with water. After 1 hr, 6 hr, and 24 hr aerial and root tissues are separated and flash frozen in liquid nitrogen prior to storage at ⁻80° C.

(z) Petals

Arabidopsis thaliana (ecotype Wassilewskija) seeds are vernalized at 4° C. for 3 days before sowing in flats containing vermiculite soil. Flats are watered placed at 20° C. in a Conviron growth chamber having 16 hr light/8 hr dark. Whole plants (used as the control) and petals from inflorescences 23-25 days after germination are harvested, flash frozen in liquid nitrogen and stored at −80° C.

(aa) Roots

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) are sterilized in full strength bleach for less than 5 min., washed more than 3 times in sterile distilled deionized water and plated on MS agar plates. The plates are placed at 4° C. for 3 nights and then placed vertically into a growth chamber having 16 hr light/8 hr dark cycles, 23° C., 70% relative humidity and ˜11,000 LUX. After 2 weeks, the roots are cut from the agar, flash frozen in liquid nitrogen and stored at ⁻80° C.

(bb) Root Hairless Mutants

Plants mutant at the rhl gene locus lack root hairs. This mutation is maintained as a heterozygote.

Seeds of Arabidopsis thaliana (ecotype Landsberg erecta) mutated at the rhl gene locus are sterilized using 30% bleach with 1 ul/ml 20% Triton-X 100 and then vernalized at 4° C. for 3 days before being plated onto GM agar plates. Plates are placed in growth chamber with 16 hr light/8 hr. dark, 23° C., 14,500-15,900 LUX, and 70% relative humidity for germination and growth.

After 7 days, seedlings are inspected for root hairs using a dissecting microscope. Mutants are harvested and the cotyledons removed so that only root tissue remained. Tissue is then flash frozen in liquid nitrogen and stored at ⁻80C.

Arabidopsis thaliana (Landsberg erecta) seedlings grown and prepared as above are used as controls.

Alternatively, seeds of Arabidopsis thaliana (ecotype Landsberg erecta), heterozygous for the rhl1 (root hairless) mutation, are surface-sterilized in 30% bleach containing 0.1% Triton X-100 and further rinsed in sterile water. They are then vernalized at 4° C. for 4 days before being plated onto MS agar plates. The plates are maintained in a growth chamber at 24° C. with 16 hr light/8 hr dark for germination and growth. After 10 days, seedling roots that expressed the phenotype (i.e. lacking root hairs) are cut below the hypocotyl junction, frozen in liquid nitrogen and stored at −80° C. Those seedlings with the normal root phenotype (heterozygous or wt) are collected as described for the mutant and used as controls.

(cc) Root Tips

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) are placed on MS plates and vernalized at 4° C. for 3 days before being placed in a 25° C. growth chamber having 16 hr light/8 hr dark, 70% relative humidity and about 3 W/m². After 6 days, young seedlings are transferred to flasks containing B5 liquid medium, 1% sucrose and 0.05 mg/l indole-3-butyric acid. Flasks are incubated at room temperature with 100 rpm agitation. Media is replaced weekly. After three weeks, roots are harvested and incubated for 1 hr with 2% pectinase, 0.2% cellulase, pH 7 before straining through a #80 (Sigma) sieve. The root body material remaining on the sieve (used as the control) is flash frozen and stored at −80° C. until use. The material that passes through the #80 sieve is strained through a #200 (Sigma) sieve and the material remaining on the sieve (root tips) is flash frozen and stored at 80° C. until use. Approximately 10 mg of root tips are collected from one flask of root culture.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 8 days. Seedlings are carefully removed from the sand and the root tips (˜2 mm long) are removed and flash frozen in liquid nitrogen prior to storage at ⁻80° C. The tissues above the root tips (˜1 cm long) are cut, treated as above and used as control tissue.

(dd) Rosette Leaves, Stems, and Siliques

Arabidopsis thaliana (ecotype Wassilewskija) seed was vernalized at 4° C. for 3 days before sowing in Metro-mix soil type 350. Flats are placed in a growth chamber having 16 hr light/8 hr dark, 80% relative humidity, 23° C. and 13,000 LUX for germination and growth. After 3 weeks, rosette leaves, stems, and siliques are harvested, flash frozen in liquid nitrogen and stored at −80° C. until use. After 4 weeks, siliques (<5 mm, 5-10 mm and >10 mm) are harvested, flash frozen in liquid nitrogen and stored at −80° C. until use. Five week old whole plants (used as controls) are harvested, flash frozen in liquid nitrogen and kept at −80° C. until RNA is isolated.

(ee) Salicylic Acid (Sa)

Seeds of Arabidopsis thaliana (ecotype Wassilewskija) are sown in trays and left at 4° C. for 4 days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr. dark, 13,000 LUX, 70% humidity, 20° C. temperature and watered twice a week with 1 L of a 1× Hoagland's solution. Approximately 1,000 14 day old plants are sprayed with 200-250 mls of 5 mM salicylic acid (solubilized in 70% ethanol) in a 0.02% solution of the detergent Silwet L-77. At 1 hr and 6 hrs after treatment, whole seedlings, including roots, are harvested within a 15 to 20 minute time period flash-frozen in liquid nitrogen and stored at ⁻80° C.

Alternatively, seeds of wild-type Arabidopsis thaliana (ecotype Columbia) and mutant CS3726 are sown in soil type 200 mixed with osmocote fertilizer and Marathon insecticide and left at 4° C. for 3 days to vernalize. Flats are incubated at room temperature with continuous light. Sixteen days post germination plants are sprayed with 2 mM SA, 0.02% SilwettL-77 or control solution (0.02% SilwettL-77. Aerial parts or flowers were harvested 1 hr, 4 hr, 6 hr, 24 hr and 3 weeks post-treatment flash frozen and stored at −80° C.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 7 days. Seedlings are carefully removed from the sand and placed in 1-liter beakers with 2 mM SA for treatment. Control plants are treated with water. After 12 hr and 24 hr, aerial and root tissues are separated and flash frozen in liquid nitrogen prior to storage at ⁻80° C.

(ff) Shoots

Sterilized wild-type Arabidopsis thaliana seeds (ecotype Wassilewskija) are sown on MS plates (0.5% sucrose, 1.5% agar) after 3 day-cold treatment. The plates are placed vertically in a Percival growth chamber (16:8 light cycles, 22° C.) so that roots grow vertically on the agar surface. The shoots or aerials, harvested after 7 d- and 14 d-growth in the chamber, are used as the experimental samples. The control sample is derived from tissues harvested from 3 week-old plants that are grown in soil in a Conviron chamber (16:8 light cycles, 22° C.), including rosettes, roots, stems, flowers, and siliques.

(gg) Shoot Apical Meristem (stm)

Arabidopsis thaliana (ecotype Landsberg erecta) plants mutant at the stm gene locus lack shoot meristems, produce aerial rosettes, have a reduced number of flowers per inflorescence, as well as a reduced number of petals, stamens and carpels, and is female sterile. This mutation is maintained as a heterozygote.

Seeds of Arabidopsis thaliana (ecotype Landsberg erecta) mutated at the stm locus are sterilized using 30% bleach with 1 ul/ml 20% Triton-X100. The seeds are vernalized at 4° C. for 3 days before being plated onto GM agar plates. Half are then put into a 22° C., 24 hr light growth chamber and half in a 24° C. 16 hr light/8 hr dark growth chamber having 14,500-15,900 LUX, and 70% relative humidity for germination and growth.

After 7 days, seedlings are examined for leaf primordia using a dissecting microscope. Presence of leaf primordia indicated a wild type phenotype. Mutants are selected based on lack of leaf primordia. Mutants are then harvested and hypocotyls removed leaving only tissue in the shoot region. Tissue is then flash frozen in liquid nitrogen and stored at −80° C.

Control tissue is isolated from 5 day old Landsberg erecta seedlings grown in the same manner as above. Tissue from the shoot region is harvested in the same manner as the stm tissue, but only contains material from the 24° C., 16 hr light/8 hr dark long day cycle growth chamber.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 8 days. Seedlings are carefully removed from the sand and the outer layers of leaf shealth removed. About 2 mm sections are cut and flash frozen in liquid nitrogen prior to storage at ⁻80° C. The tissues above the shoot apices (˜1 cm long) are cut, treated as above and used as control tissue.

(hh) Siliques

Wild type Arabidopsis thaliana (ecotype Wassilewskija) seeds are sown in moistened soil mix, metromix 200 with osmocote, and stratified at 4° C. for 3 days in dark. Flats are placed in a Conviron growth chamber maintained at 16 h light (22° C.), 8 h dark (20° C.) and 70% humidity. After 3 weeks, siliques (<5 mm long) are collected in liquid nitrogen. The control samples are 3-week old whole plants (including all tissue types) grown in the same Conviron growth chamber.

(ii) Wounding

Seeds of Arabidopsis thaliana (Wassilewskija) are sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 70% humidity and 20° C. After 14 days, the leaves are wounded with forceps. Aerial tissues are harvested 1 hour and 6 hours after wounding. Aerial tissues from unwounded plants serve as controls. Tissues are flash-frozen in liquid nitrogen and stored at ⁻80° C.

Seeds of maize hybrid 35A (Pioneer) are sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats are watered every three days for 7 days. Seedlings are wounded (one leaf nicked by scissors) and placed in 1-liter beakers of water for treatment. Control plants are treated not wounded. After 1 hr and 6 hr aerial and root tissues are separated and flash frozen in liquid nitrogen prior to storage at ⁻80° C.

2. Microarray Hybridization Procedures

Microarray technology provides the ability to monitor mRNA transcript levels of thousands of genes in a single experiment. These experiments simultaneously hybridize two differentially labeled fluorescent cDNA pools to glass slides that have been previously spotted with cDNA clones of the same species. Each arrayed cDNA spot will have a corresponding ratio of fluorescence that represents the level of disparity between the respective mRNA species in the two sample pools. Thousands of polynucleotides can be spotted on one slide, and each experiment generates a global expression pattern.

The microarray consists of a chemically coated microscope slide, referred herein as a “chip” with numerous polynucleotide samples arrayed at a high density. The poly-L-lysine coating allows for this spotting at high density by providing a hydrophobic surface, reducing the spreading of spots of DNA solution arrayed on the slides. Glass microscope slides (Gold Seal #3010 manufactured by Gold Seal Products, Portsmouth, N.H., USA) are coated with a 0.1% W/V solution of Poly-L-lysine (Sigma, St. Louis, Mo.).

Polynucleotides are amplified from Arabidopsis cDNA clones using insert specific probes. The resulting 100 uL PCR reactions are purified and PCR products from cDNA clones are spotted onto the poly-L-Lysine coated glass slides using an arrangement of quill-tip pins (ChipMaker 3 spotting pins; Telechem, International, Inc., Sunnyvale, Calif., USA) and a robotic arrayer (PixSys 3500, Cartesian Technologies, Irvine, Calif., USA). Slides containing maize sequences are purchased from Agilent Technology (Palo Alto, Calif. 94304).

After arraying, slides are processed through a series of steps—rehydration, UV cross-linking, blocking and denaturation—required prior to hybridization. Slides are rehydrated by placing them over a beaker of warm water (DNA face down), for 2-3 sec, to distribute the DNA more evenly within the spots, and then snap dried on a hot plate (DNA side, face up). The DNA is then cross-linked to the slides by UV irradiation (60-65 mJ; 2400 Stratalinker, Stratagene, La Jolla, Calif., USA).

The Hybridization process begins with the isolation of mRNA from the two tissues (see “Isolation of total RNA” and “Isolation of mRNA”, below) in question followed by their conversion to single stranded cDNA (see “Generation of probes for hybridization”, below). The cDNA from each tissue is independently labeled with a different fluorescent dye and then both samples are pooled together. This final differentially labeled cDNA pool is then placed on a processed microarray and allowed to hybridize (see “Hybridization and ish conditions”, below).

mRNA is isolated using the Qiagen Oligotex mRNA Spin-Column protocol (Qiagen, Valencia, Calif.) or using the Stratagene Poly(A) Quik mRNA Isolation Kit (Startagene, La Jolla, Calif.).

Plasmid DNA is isolated from the following yeast clones using Qiagen filtered maxiprep kits (Qiagen, Valencia, Calif.): YAL022c(Fun26), YAL031c(Fun21), YBR032w, YDL131w, YDL182w, YDL194w, YDL196w, YDR050c and YDR116c. Plasmid DNA is linearized with either BsrBI (YAL022c(Fun26), YAL031c(Fun21), YDL131w, YDL182w, YDL194w, YDL196w, YDR050c) or AflIII (YBR032w, YDR116c) and isolated.

Generation of Probes for Hybridization

Generation of Labeled Probes for Hybridization from First-Strand cDNA

Hybridization probes are generated from isolated mRNA using an Atlas™ Glass Fluorescent Labeling Kit (Clontech Laboratories, Inc., Palo Alto, Calif., USA). This entails a two step labeling procedure that first incorporates primary aliphatic amino groups during cDNA synthesis and then couples fluorescent dye to the cDNA by reaction with the amino functional groups.

The probe is purified using a Qiagen PCR cleanup kit (Qiagen, Valencia, Calif., USA), and eluted with 100 ul EB (kit provided). The sample is loaded on a Microcon YM-30 (Millipore, Bedford, Mass., USA) spin column and concentrated to 4-5 ul in volume.

Probes for the maize microarrays are generated using the Fluorescent Linear Amplification Kit (cat. No. G2556A) from Agilent Technologies (Palo Alto, Calif.).

Maize microarrays are hybridized according to the instructions included Fluorescent Linear Amplification Kit (cat. No. G2556A) from Agilent Technologies (Palo Alto, Calif.).

The chips are scanned using a ScanArray 3000 or 5000 (General Scanning, Watertown, Mass., USA). The chips are scanned at 543 and 633 nm, at 10 um resolution to measure the intensity of the two fluorescent dyes incorporated into the samples hybridized to the chips.

The images generated by scanning slides consisted of two 16-bit TIFF images representing the fluorescent emissions of the two samples at each arrayed spot. These images are then quantified and processed for expression analysis using the data extraction software Imagene™ (Biodiscovery, Los Angeles, Calif., USA). Imagene output is subsequently analyzed using the analysis program Genespring™ (Silicon Genetics, San Carlos, Calif., USA). In Genespring, the data is imported using median pixel intensity measurements derived from Imagene output. Background subtraction, ratio calculation and normalization are all conducted in Genespring. Normalization is achieved by breaking the data in to 32 groups, each of which represented one of the 32 pin printing regions on the microarray. Groups consist of 360 to 550 spots. Each group is independently normalized by setting the median of ratios to one and multiplying ratios by the appropriate factor.

An additional deposit of an E. coli Library, E. coliLibA021800, was made at the American Type Culture Collection in Manassas, Va., USA on Feb. 22, 2000 to meet the requirements of Budapest Treaty for the international recognition of the deposit of microorganisms. This deposit was assigned ATCC accession no. PTA-1411. Additionally, ATCC Library deposits; PTA-1161, PTA-1411 and PTA-2007 were made at the American Type Culture Collection in Manassas, Va., USA on; Jan. 7, 2000, Feb. 23, 2000 and Jun. 8, 2000 respectively, to meet the requirements of Budapest Treaty for the international recognition of the deposit of microorganisms.

The invention being thus described, it will be apparent to one of ordinary skill in the art that various modifications of the materials and methods for practicing the invention can be made. Such modifications are to be considered within the scope of the invention as defined by the following claims.

The scientific periodical and patent publications that follow are discussed in the Specification and are hereby incorporated by reference in their entirety:

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1. An isolated nucleic acid molecule comprising: a) a nucleic acid having a nucleotide sequence which encodes an amino acid sequence exhibiting at least 40% sequence identity to an amino acid sequence encoded by (1) a nucleotide sequence described in the Sequence Listing or a fragment thereof; or (2) a complement of a nucleotide sequence shown in the Sequence Listing or a fragment thereof; b) a nucleic acid which is the reverse of the nucleotide sequence according to subparagraph (a), such that the reverse nucleotide sequence has a sequence order which is the reverse of the sequence order of the nucleotide sequence according to subparagraph (a); c) a nucleic acid capable of hybridizing to a nucleic acid having a sequence selected from the group consisting of: (1) a nucleotide sequence which is shown in the Sequence Listing; and a nucleotide sequence which is complementary to a nucleotide sequence shown in the Sequence Listing, under conditions that permit formation of a nucleic acid duplex at a temperature from about 40° C. and 48° C. below the melting temperature of the nucleic acid duplex, with the proviso that said nucleotide sequence is not any of the sequences described in the Tables of any of Patent Publication Nos. WO 200040695, CA 2300692 A1, EP 1033405 A2, CA 2302828 A1 and EP 1059354 A2 and any proteins listed in the application that are identified by gi number or otherwise as being from the non-redundant GenBank CDS translations or Protein Database (PDB) or (PIR-International) Database (PIR).
 2. An isolated nucleic acid molecule comprising a nucleic acid having a nucleotide sequence which exhibits at least 65% sequence identity to a) a nucleotide sequence shown in the Sequence Listing or a fragment thereof; or b) a complement of a nucleotide sequence described in the Sequence Listing or a fragment thereof, with the proviso that said nucleotide sequence is not any of the sequences described in the Tables of any of Patent Publication Nos. WO 200040695, CA 2300692 A1, EP 1033405 A2, CA 2302828 A1 and EP 1059354 A2 and any proteins listed in the application that are identified by gi number or otherwise as being from the non-redundant GenBank CDS translations or Protein Database (PDB) or (PIR-International) Database (PIR).
 3. The nucleic acid molecule according to claim 1, wherein said nucleic acid comprises an open reading frame.
 4. A vector construct comprising: a) a first nucleic acid having a regulatory sequence capable of causing transcription and/or translation; and b) a second nucleic acid having the sequence of the isolated nucleic acid molecule according to claim 1; wherein said first and second nucleic acids are operably linked and wherein said second nucleic acid is heterologous to any element in said vector construct.
 5. The vector construct according to claim 4, wherein said first nucleic acid is native to said second nucleic acid.
 6. The vector construct according to claim 4, wherein said first nucleic acid is heterologous to said second nucleic acid.
 7. A host cell comprising an isolated nucleic acid molecule according to claim 1, wherein said nucleic acid molecule is flanked by exogenous sequence.
 8. A host cell comprising a vector construct of claim
 4. 9. An isolated polypeptide comprising an amino acid sequence a) exhibiting at least 40%, 75%, 85%, or 90% sequence identity of an amino acid sequence encoded by a sequence shown in the Sequence Listing or a fragment thereof; and b) capable of exhibiting at least one of the biological activities of the polypeptide encoded by said nucleotide sequence shown in the Sequence Listing or a fragment thereof, with the proviso that said nucleotide sequence is not any of the sequences described in the Tables of any of Patent Publication Nos. WO 200040695, CA 2300692 A1, EP 1033405 A2, CA 2302828 A1 and EP 1059354 A2 and any proteins listed in the application that are identified by gi number or otherwise as being from the non-redundant GenBank CDS translations or Protein Database (PDB) or (PIR-International) Database (PIR).
 10. An antibody capable of binding the isolated polypeptide of claim
 9. 11. A method of introducing an isolated nucleic acid into a host cell comprising: a) providing an isolated nucleic acid molecule according to claim 1; and b) contacting said isolated nucleic with said host cell under conditions that permit insertion of said nucleic acid into said host cell.
 12. A method of transforming a host cell which comprises contacting a host cell with a vector construct according to claim
 4. 13. A method of modulating transcription and/or translation of a nucleic acid in a host cell comprising: a) providing the host cell of claim 7; and b) culturing said host cell under conditions that permit transcription or translation.
 14. A method for detecting a nucleic acid in a sample which comprises: a) providing an isolated nucleic acid molecule according to claim 1; b) contacting said isolated nucleic acid molecule with a sample under conditions which permit a comparison of the sequence of said isolated nucleic acid molecule with the sequence of DNA in said sample; and c) analyzing the result of said comparison.
 15. A plant or cell of a plant which comprises a nucleic acid molecule according to claim 1 which is exogenous or heterologous to said plant or plant cell.
 16. A plant or cell of a plant which comprises a vector construct according to claim
 4. 17. A plant which has been regenerated from a plant cell according to claim
 15. 18. A plant which has been regenerated from a plant cell according to claim
 16. 